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% cachedas -servername tdas -auto -cachefile ~/.embossdata/qatests.server.dasregistry host = www.dasregistry.org path = /das/sources port = 80 DAS sources and descriptions DS_111 cath The CATH database annotates PDB structures with CATH structural domains as derived from a combination of automatic and manually methods. DS_112 structure A reference server for protein structure annotations. Serves 3D coordinates of protein structures. DS_114 signalp SignalP (http://www.cbs.dtu.dk/services/SignalP) predictions for UniProt. DS_115 netphos NetPhos (http://www.cbs.dtu.dk/services/NetPhos) predictions for UniProt. DS_118 prop ProP (http://www.cbs.dtu.dk/services/ProP) predictions for UniProt. DS_119 transmem_pred Membrane protein annotation. Presenty This DAS server contains UNIPROT and IPI human proteins. The annotation si done using 4 different predictors: TMHMM2.0, MEMSAT, ENSEMBLE_1.0 and PRODIV_TMHMM_0.91 DS_120 Uniprot 2010_09 SUPERFAMILY domain annotation for Uniprot 2010_09. DS_121 secretomep SecretomeP (http://www.cbs.dtu.dk/services/SecretomeP) predictions for UniProt. DS_126 Compara Phenotypes Phenotypes linked through homologues and protein families DS_129 Takifugu rubripes 59_4m (all transcripts) SUPERFAMILY domain annotation for Takifugu rubripes 59_4m (all transcripts). DS_133 cbs_ptm Aggregation server for CBS predictions related to post-translational modifications of proteins. DS_134 cbs_func Aggregation server for CBS predictions related to protein function and structure. DS_146 ensp_pdb_mapping If you click on a feature of this DAS track, SPICE can be launched from ENSEMBL. - Mapping of ENSP protein sequences to protein structures. Based on the Compara ENSP - UniProt and the MSD - UniProt to PDB mapping. DS_150 s3dm Small hydrogen bonded motifs, beta turn like. DS_154 nscsnp deleterious Machine learning approach used SWISSPROT variants annotated as disease/neutral as training dataset. Predictions made on all ENSEMBL nscSNPs as to their disease status PMID: 16630345 DS_180 IMGT DAS Sources Homo sapiens IG and TR genes located using IMGT reference sequences. DS_181 snp_hsa/bioinfo.cipf DS_182 ens_zfish7_array ens_zfish7_array DS_183 ens_zfish7_enhancer ens_zfish7_enhancer DS_187 lipop LipoP (www.cbs.dtu.dk/ser vices/LipoP) predictions for UniProt. DS_188 netnes NetNES (www.cbs.dtu.dk/ser vices/NetNES) predictions for UniProt. DS_190 ens_zfish7_tilling ens_zfish7_tilling DS_191 hsa35pep A reference and annotation server for Ensembl peptides. Provides exon structure and SNPs as features DS_192 alig_uniprot_ensp an alignment server that provides alignments between Ensembl peptides (ENSP) and UniProt DS_193 ens_35_segdup_washu Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_194 ens_35_segdup_toronto Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_195 ens_35_segdup_wssd Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_196 ens_35_segdup_sanger Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_197 ens_35_segdup_washufilt Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_199 CSA - literature Catalytic Site Atlas (http://www.ebi.ac.uk/thornton-srv/databases/CSA/) literature annotations mapped onto Uniprot. DS_200 CSA - extended Catalytic Site Atlas (http://www.ebi.ac.uk/thornton-srv/databases/CSA/) literature annotations extended to putative sites by homology. DS_210 SMART SMART domain annotations for Uniprot/Ensembl DS_212 FunCUT FunCUT is a method for the automatic annotation of protein function based on family identification. DS_216 SAS protein binding Putative protein-protein binding sites by homology with those observed in crystallized protein structures. DS_217 SAS ligand binding Putative ligand binding sites by homology with those observed in crystallized protein structures. DS_218 SAS DNA binding Putative protein-DNA binding sites by homology with those observed in crystallized protein structures. DS_222 ens_ncbi_35_omimg OMIM morbidmap data mapped to NCBI35 assembly locations DS_224 toronto_poly Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_226 GENCODE sequences ENCODE peptide reference server. DS_227 GENCODE alignments Local and global gapped alignments with UniProt and UniParc using Exonerate 1.0. DS_228 GENCODE Pfam Putative domains predicted using Pfam HMMs on ENCODE peptides. DS_229 GENCODE PDBsum Structurally derived information from PDBsum mapped by homology to ENCODE peptides (http://www.ebi.ac.uk/thornton-srv/ENCODE/pdbsum.html). DS_237 3D-EM Reference server for 3D-EM volume maps data from EMDB. DS_238 3D-EM_EMDB Annotation server for 3D-EM volume data. Most textual data parsed from EMDB. DS_239 3D-EM_Fitting Alignment server for fitting experiments (PDB structures into 3D-EM volumes). DS_241 pfam The Pfam DAS services offers sequence, feature and types capabilities. The features response returns Pfam-A, Pfam-B domains and other features like Active site, transmembrane region, disulfide bridges, coiled coil, signal peptide and low complexity region for the sequences. The sequence database (pfamseq) is the same as the current version of Pfam. It is essentially comprised of Uniprot with artificial chimeric sequences removed. DS_248 HGNC The HGNC (HUGO Gene Nomenclature Committee) DAS Reference Server serves up-to-date approved gene symbols and names for human genes from the latest HGNC dataset, mapped via Entrez Gene ID. DS_251 Ensembl Human Genes The Ensembl human Gene_ID reference source, serving sequences and non-location features. DS_312 ens_zfish7_baxendale_est ens_zfish7_baxendale_est DS_313 ens_zfish7_carp_est ens_zfish7_carp_est DS_327 InterPro InterPro (http://www.ebi.ac.uk/interpro/), a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. This data source contains all InterPro member database signature matches to UniProtKB protein sequences. DS_334 GSC_mRNA Comparison between human and tetraodon genomes and Genoscope mRNAs sequences (for details see http://www.genoscope.cns.fr/cgi-bin/ggb/BioSapiens/gbrowse/GSC_mRNA?help=citations). DS_335 ExoFish Exofish (Exon Finding by Sequences Homology, http://www.genoscope.cns.fr/externe/tetraodon/what_exofish.html) is a genomic tool based on the assumption that coding regions are more conserved than non-coding regions through evolution. Therefore, if it compare the genomes of two species, regions of homology should reveal coding regions. Exofish is performed with sequences of Tetraodon nigroviridis, and calibrated to annotate human genome. DS_337 viraldas_hiv1_hxb2 The ViralDAS Server for HIV-1 is the first DAS Server for a viral genome. It was specifically adapted from the default DAS server type to meet the requirements posed by a viral genome: in addition to the genome, transcripts and proteins which are usually found in eukaryotic DAS servers, it has been enhanced to display polyproteins and their cleaved products. DS_341 everest A positional automatic identification and clustering of protein domains. DS_342 protonet ProtoNet (http://www.protonet.cs.huji.ac.il) provides automatic hierarchical classification of protein sequences (non-positional protein annotations). DS_359 Phobius Phobius - combined prediction of transmembrane topology and signal peptides for Uniprot. http://phobius.cgb.ki.se/ or http://phobius.binf.ku.dk/ ENSEMBL_6_BROADD2 Canis_familiaris.BROADD2.prediction_transcript Annotation source for Canis_familiaris prediction_transcript ENSEMBL_6_JGI2 Ciona_intestinalis.JGI2.prediction_transcript Annotation source for Ciona_intestinalis prediction_transcript ENSEMBL_6_CSAV2.0 Ciona_savignyi.CSAV2.0.prediction_transcript Annotation source for Ciona_savignyi prediction_transcript ENSEMBL_6_TENREC Echinops_telfairi.TENREC.prediction_transcript Annotation source for Echinops_telfairi prediction_transcript ENSEMBL_6_HEDGEHOG Erinaceus_europaeus.HEDGEHOG.prediction_transcript Annotation source for Erinaceus_europaeus prediction_transcript ENSEMBL_6_CAT Felis_catus.CAT.prediction_transcript Annotation source for Felis_catus prediction_transcript ENSEMBL_6_WASHUC2 Gallus_gallus.WASHUC2.prediction_transcript Annotation source for Gallus_gallus prediction_transcript ENSEMBL_6_BROADS1 Gasterosteus_aculeatus.BROADS1.prediction_transcri Annotation source for Gasterosteus_aculeatus prediction_transcript ENSEMBL_6_MMUL_1 Macaca_mulatta.MMUL_1.prediction_transcript Annotation source for Macaca_mulatta prediction_transcript ENSEMBL_6_OANA5 Ornithorhynchus_anatinus.OANA5.prediction_transcri Annotation source for Ornithorhynchus_anatinus prediction_transcript ENSEMBL_6_CHIMP2.1 Pan_troglodytes.CHIMP2.1.prediction_transcript Annotation source for Pan_troglodytes prediction_transcript ENSEMBL_6_RGSC3.4 Rattus_norvegicus.RGSC3.4.prediction_transcript Annotation source for Rattus_norvegicus prediction_transcript ENSEMBL_6_FUGU4 Takifugu_rubripes.FUGU4.prediction_transcript Annotation source for Takifugu_rubripes prediction_transcript ENSEMBL_6_TREESHREW Tupaia_belangeri.TREESHREW.prediction_transcript Annotation source for Tupaia_belangeri prediction_transcript DS_401 PPDB_das PPDB (http://ppdb.tc.cornell.edu) is a specialized proteome database dedicated to plant plastids. It is a joint project between Klaas J. van Wijk Lab and the Computational Biology Service Unit of Cornell University. The main objective is to provide a centralized, curated, data deposit for predicted and experimentally determined plastid proteins in Arabidopsis thaliana and maize (Zea mays), their annotated functions, as well as their experimental and predicted molecular and biophysical properties. All gene models in the Arabidopsis nuclear and organellar genomes as annotated by TAIR, as well as all maize EST assemblies (ZmGI) and maize genome sequence assemblies (AZM) as annotated by TIGR. The das server of PPDB provide the peptide sequences that are identified in each protein sequences. DS_405 SNPbox SNPbox analysis of all Ensembl exons for homo sapiens DS_406 OMA OMA (Orthology Prediction from ETH Zurich) DS_407 pfamFullAlign Retrieves the full sequence alignments for a Pfam entry. DS_408 pfamSeedAlign Retrieves the seed sequence alignments for a Pfam entry. DS_409 uniprot DAS 1 reference server for sequence and features from UniProt. UniProt (Universal Protein Resource) is the worlds most comprehensive catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. Alternative to the 'aristotle' dsn on the same DAS server. Note: New version launched on 05/09/2008. Support for keywords(KW) and comments(CC). Ontologies have also been introduced into the annotations. DS_410 IPI DAS 1 reference server for sequence and features from IPI. IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI: 1. effectively maintains a database of cross references between the primary data sources 2. provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) 3. maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources. Alternative to the aristotle dsn on the same DAS server (DS_109) DS_411 IPI Tryptic Peptides Theoretical tryptic peptides based upon a complete and successful digest of the requested proteins with trypsin. DS_412 UniProt GO Annotation The GOA project aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI) and is a central dataset for other major multi-species databases; such as Ensembl and NCBI. DS_413 UniProt Tryptic Peptides Theoretical tryptic peptides based upon a complete and successful digest of the requested proteins with trypsin. DS_414 uniparc UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences extracted from public databases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, PIR-PSD, EMBL, EMBL WGS, Ensembl, IPI, PDB, PIR-PSD, RefSeq, FlyBase, WormBase, H-Invitational Database, TROME database, European Patent Office proteins, United States Patent and Trademark Office proteins (USPTO) and Japan Patent Office proteins. DS_415 RSBP Parts RSBP Parts ENSEMBL_6_BROADO5 Monodelphis_domestica.BROADO5.prediction_transcrip Annotation source for Monodelphis_domestica prediction_transcript ENSEMBL_6_BUSHBABY1 Otolemur_garnettii.BUSHBABY1.prediction_transcript Annotation source for Otolemur_garnettii prediction_transcript ENSEMBL_6_COMMON_SHREW1 Sorex_araneus.COMMON_SHREW1.prediction_transcript Annotation source for Sorex_araneus prediction_transcript ENSEMBL_6_SQUIRREL Spermophilus_tridecemlineatus.SQUIRREL.prediction_ Annotation source for Spermophilus_tridecemlineatus prediction_transcript VEGA_3_Cfam_VEGA-clone Canis_familiaris.VEGA-clone.transcript Annotation source (returns clones) for Canis_familiaris transcript VEGA_4_Cfam_VEGA-clone Canis_familiaris.VEGA-clone.translation Annotation source (returns clones) for Canis_familiaris translation VEGA_3_Sscr_VEGA-clone Sus_scrofa.VEGA-clone.transcript Annotation source (returns clones) for Sus_scrofa transcript VEGA_4_Sscr_VEGA-clone Sus_scrofa.VEGA-clone.translation Annotation source (returns clones) for Sus_scrofa translation DS_442 Cosmic Transcripts Transcripts from Cosmic DS_443 Cosmic Transcripts Transcripts from Cosmic mapped to Human NCBI 36 DS_444 Cosmic Mutations Mutations from Cosmic DS_445 Cosmic Mutations Mutations from Cosmic mapped to Human NCBI 36 DS_446 Gene3D-CATH Domain Assigments HMM-based domain predictions derived from the CATH manually curated structural domain database. DS_447 CATH Structural Domains in UniProt Manually curated structural domain assignments sourced from CATH and the wwPDB and mapped to UniProt. DS_448 Gene3D Protein Families Gene3D provides a clustering of most sequences in UniProt. Each family is then further subclustered at 10 sequence identity levels providing an 11-part code. DS_449 SPLIT 4.0 Transmembrane Predictions Transmembrane helices as predicted by the SPLIT 4.0 software (Juretic et al). DS_490 HUGO text mining PubMed text-mining via HUGO symbol DS_493 eQTL cis RI fat Expression Quantitative Trait Loci (cis) for Rattus norvegicus DS_494 eQTL cis RI kidney Expression Quantitative Trait Loci (cis) for Rattus norvegicus DS_495 eQTL trans RI fat Expression Quantitative Trait Loci (trans) for Rattus norvegicus DS_496 eQTL trans RI kidney Expression Quantitative Trait Loci (trans) for Rattus norvegicus DS_497 Sjoblom Breast and Colon Cancer associated Mutations described by Sjoblom et al. (Science. 2006,314(5797):268-74) DS_498 HomoMINT Persico, M. et al. (2005). HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics, 6 Suppl 4:S21. DS_499 CCSB-HI1 Rual, J.-F. et al. (2005). Towards a proteome-scale map of the human protein-protein interaction network. Nature, 437(7062):1173-1178. DS_500 Sanger Lehner, B. and Fraser, A. G. (2004). A first-draft human protein interaction map. Genome Biol, 5(9):R63. DS_501 Sanger-core Lehner, B. and Fraser, A. G. (2004). A first-draft human protein interaction map. Genome Biol, 5(9):R63. DS_502 POINT Huang, T.-W. et al. (2004). POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome. Bioinformatics, 20(17):3273-3276. DS_503 OPHID Brown, K. R. and Jurisica, I. (2005). Online predicted human interaction database. Bioinformatics, 21(9):2076-2082. DS_504 MDC Stelzl, U. et al. (2005). A human protein-protein interaction network: a resource for annotating the proteome. Cell, 122(6):957-968. DS_505 HiMAP Rhodes, D. R. et al. (2005). Probabilistic model of the human protein-protein interaction network. Nat Biotechnol, 23(8):951-959. DS_506 HiMAP-core Rhodes, D. R. et al. (2005). Probabilistic model of the human protein-protein interaction network. Nat Biotechnol, 23(8):951-959. DS_507 Bioverse McDermott, J. et al. (2005). Functional annotation from predicted protein interaction networks. Bioinformatics, 21(15):3217-3226. DS_509 zTrap Gene and enhancer trapping in zebrafish DS_510 HMMTOP HMMTOP 2.1 - prediction of transmembrane helices and topology of proteins. Written by Gabor E. Tusnady DS_511 PHDhtm PHDhtm 2.0 - neural-network-based transmembrane predictor. Written by Burkhard Rost DS_513 toppred Toppred 1.0 - transmembrane topology predictor. Written by Eric Deveaud and Katja Schuerer, based on an algorithm by Gunnar von Heijne. DS_517 PHDsec PHDsec 2.0 - neural-network-based secondary structure predictor. Written by Burkhard Rost. DS_518 PHDacc PHDacc 2.0 - neural-network-based solvent accessibility predictor. Written by Burkhard Rost. DS_524 ECARUCA Registered ECARUCA abberations smaller than 30Mb DS_525 Phosida Phosida - Phosphorylation Site Database DS_526 3did Stein et al. (2005). 3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Res, 33(Database issue):D413–D417. DS_527 interdom Ng et al. (2003). Integrative approach for computationally inferring protein domain interactions. Bioinformatics, 19(8):923–929. DS_528 ldsc Lee et al. (2006). An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics, 7:269. DS_529 ldsc-core Lee et al. (2006). An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics, 7:269. DS_530 apmm1 Wang et al. (2007). Analysis on multi-domain cooperation for predicting protein-protein interactions. BMC Bioinformactics, 8(1):391 DS_531 apmm2 Wang et al. (2007). Analysis on multi-domain cooperation for predicting protein-protein interactions. BMC Bioinformactics, 8(1):391 DS_532 llz Liu et al. (2005). Inferring protein-protein interactions through high-throughput interaction data from diverse organisms. Bioinformatics, 21(15):3279–3285. DS_533 dima-dpea Pagel et al. (2008). DIMA 2.0–predicted and known domain interactions. Nucleic Acids Res, 36, D651–D655. DS_534 dima-string Pagel et al. (2008). DIMA 2.0–predicted and known domain interactions. Nucleic Acids Res, 36, D651–D655. DS_535 dima-dprof Pagel et al. (2008). DIMA 2.0–predicted and known domain interactions. Nucleic Acids Res, 36, D651–D655. DS_536 dpea Riley et al. (2005). Inferring protein domain interactions from databases of interacting proteins. Genome Biol, 6(10):R89. DS_537 lp Guimaraes. et al. (2006). Predicting domain-domain interactions using a parsimony approach. Genome Biol, 7(11):R104. DS_538 RDFF Chen et al. (2005). Prediction of protein-protein interactions using random decision forest framework. Bioinformatics, 21(24):4394-400. DS_539 rcdp50 Jothi et al. (2006). Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J Mol Biol, 362(4):861-75. DS_540 tw Wuchty et al. (2006). Topology and weights in a protein domain interaction network-a novel way to predict protein interactions. BMC Genomcis, 7:122. DS_541 FunSimMat 2.1 Schlicker and Albrecht. (2008). FunSimMat: a comprehensive functional similarity database. Nucleic Acids Res, 36, D434–D439. DS_542 Domain support Protein interactions that are supported by underlying domain interactions as reported in iPfam. DS_544 merops merops DS_546 UCSC Gencode UCSC Gencode related tracks DS_548 novelloci 327 novel gene fragments provided by Mark Diekhans DS_549 Gene Expression Atlas European Bioinformatics Institute (EMBL-EBI) Gene Expression Atlas. The Gene Expression Atlas is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. DS_550 otter manual annotations A DAS source that provides access to the manual annotation data inside the Otter database in NCBI36 coordinates. DS_553 translated otter manual annotations A DAS source that provides the translations of the manual annotation data inside the Otter database. DS_557 ASTD human exons ASTD exon features grouped into transcripts, offered on human chromosome co-ordinates. DS_558 ASTD mouse exons ASTD exon features grouped into transcripts, offered on mouse chromosome co-ordinates. DS_559 ASTD rat exons ASTD exon features grouped into transcripts, offered on rat chromosome co-ordinates. DS_560 ASTD human SNPs ASTD SNP features, offered on human chromosome co-ordinates. DS_561 ASTD mouse SNPs ASTD SNP features, offered on mouse chromosome co-ordinates. DS_562 ASTD rat SNPs ASTD SNP features, offered on rat chromosome co-ordinates. DS_564 PInS Bordner and Gorin (2008). Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces. BMC Bioinformatics, 9:234. DS_566 GRC region human genome NCBI36 Region reported to the Genome Reference Consortium NCBI36 DS_567 Human miRNAs A DAS source that provides access to the annotation data of primary transcripts of human miRNAs DS_568 Mouse miRNAs A DAS source that provides access to the annotation data of primary transcripts of mouse miRNAs DS_569 Rat miRNAs A DAS source that provides access to the annotation data of primary transcripts of rat miRNAs DS_570 hydra_ptg_p53_p19_M37 hydra_ptg_p53_p19_M37 mutations DS_571 CONGO de novo protein-coding exon predictions based on evolutionary signatures in 18 mammalian genomes (preliminary data, not for use in production pipelines) DS_572 JAX Mouse Data Mouse Genome Informatics data DS_579 Consensus Pseudogenes Pseudogenes where both Yales PseudoPipe and UCSCs RetroFinder algorithms agree. DS_580 otter manual annotations transcript sequences A DAS source that provides the transcript sequences of the manual annotation data from the Otter database. DS_581 SWISS-MODEL Repository SWISS-MODEL Repository DS_582 GNF Tissue Atlas Rat Tissue Expression data from the Genomics Institute of the Novartis Research Foundation. DS_583 GAD Genetic Association Database (diseases) DS_585 eQTL Sanger Expression Quantitative Trait Loci from the Sanger Institute DS_586 MeDIP-chip B-cells DNA methylation landscape for B-cells, assayed using methyl DNA immunoprecipitation (MeDIP), a Nimblegen oligonucleotide array and Bayesian Tool for Methylation Analysis (Batman). DS_587 MeDIP-chip CD4 T-cells DNA methylation landscape for CD4 T-cells, assayed using methyl DNA immunoprecipitation (MeDIP), a Nimblegen oligonucleotide array and Bayesian Tool for Methylation Analysis (Batman). DS_588 MeDIP-chip CD8 T-cells DNA methylation landscape for CD8 T-cells, assayed using methyl DNA immunoprecipitation (MeDIP), a Nimblegen oligonucleotide array and Bayesian Tool for Methylation Analysis (Batman). DS_589 MeDIP-chip Cervix DNA methylation landscape for Cervix, assayed using methyl DNA immunoprecipitation (MeDIP), a Nimblegen oligonucleotide array and Bayesian Tool for Methylation Analysis (Batman). DS_590 MeDIP-chip Colon DNA methylation landscape for Colon, assayed using methyl DNA immunoprecipitation (MeDIP), a Nimblegen oligonucleotide array and Bayesian Tool for Methylation Analysis (Batman). DS_591 MeDIP-chip GM06990 DNA methylation landscape for GM06990, assayed using methyl DNA immunoprecipitation (MeDIP), a Nimblegen oligonucleotide array and Bayesian Tool for Methylation Analysis (Batman). DS_592 MeDIP-chip Liver DNA methylation landscape for Liver, assayed using methyl DNA immunoprecipitation (MeDIP), a Nimblegen oligonucleotide array and Bayesian Tool for Methylation Analysis (Batman). DS_593 MeDIP-chip Lung DNA methylation landscape for Lung, assayed using methyl DNA immunoprecipitation (MeDIP), a Nimblegen oligonucleotide array and Bayesian Tool for Methylation Analysis (Batman). DS_594 MeDIP-chip Pancreas DNA methylation landscape for Pancreas, assayed using methyl DNA immunoprecipitation (MeDIP), a Nimblegen oligonucleotide array and Bayesian Tool for Methylation Analysis (Batman). DS_595 MeDIP-chip Placenta DNA methylation landscape for Placenta, assayed using methyl DNA immunoprecipitation (MeDIP), a Nimblegen oligonucleotide array and Bayesian Tool for Methylation Analysis (Batman). DS_596 MeDIP-chip Prostate DNA methylation landscape for Prostate, assayed using methyl DNA immunoprecipitation (MeDIP), a Nimblegen oligonucleotide array and Bayesian Tool for Methylation Analysis (Batman). DS_597 MeDIP-chip Rectum DNA methylation landscape for Rectum, assayed using methyl DNA immunoprecipitation (MeDIP), a Nimblegen oligonucleotide array and Bayesian Tool for Methylation Analysis (Batman). DS_598 MeDIP-chip Skeletal Muscle DNA methylation landscape for Skeletal Muscle, assayed using methyl DNA immunoprecipitation (MeDIP), a Nimblegen oligonucleotide array and Bayesian Tool for Methylation Analysis (Batman). DS_599 MeDIP-chip Sperm DNA methylation landscape for Sperm, assayed using methyl DNA immunoprecipitation (MeDIP), a Nimblegen oligonucleotide array and Bayesian Tool for Methylation Analysis (Batman). DS_600 MeDIP-chip Uterus DNA methylation landscape for Uterus, assayed using methyl DNA immunoprecipitation (MeDIP), a Nimblegen oligonucleotide array and Bayesian Tool for Methylation Analysis (Batman). DS_601 MeDIP-chip Whole Blood DNA methylation landscape for Whole Blood, assayed using methyl DNA immunoprecipitation (MeDIP), a Nimblegen oligonucleotide array and Bayesian Tool for Methylation Analysis (Batman). ENSEMBL_6_Btau_4.0 Bos_taurus.Btau_4.0.prediction_transcript Annotation source for Bos_taurus prediction_transcript ENSEMBL_6_EquCab2 Equus_caballus.EquCab2.prediction_transcript Annotation source for Equus_caballus prediction_transcript ENSEMBL_6_micMur1 Microcebus_murinus.micMur1.prediction_transcript Annotation source for Microcebus_murinus prediction_transcript ENSEMBL_6_pika Ochotona_princeps.pika.prediction_transcript Annotation source for Ochotona_princeps prediction_transcript ENSEMBL_6_TETRAODON8 Tetraodon_nigroviridis.TETRAODON8.prediction_trans Annotation source for Tetraodon_nigroviridis prediction_transcript DS_634 BM_hydrophobicity A hydrophobicity plot using the Black-Mould algorithm (Black, S.D. and Mould, D.R. 1991. Anal. Biochem. 193, 72-82) DS_635 KD_hydrophobicity A hydrophobicity plot using the Kyte-Doolittle algorithm (Kyte, J, Doolittle, RF. 1982. J Mol Biol 157:105-132). ENSEMBL_6_cavPor3 Cavia_porcellus.cavPor3.prediction_transcript Annotation source for Cavia_porcellus prediction_transcript ENSEMBL_6_dipOrd1 Dipodomys_ordii.dipOrd1.prediction_transcript Annotation source for Dipodomys_ordii prediction_transcript ENSEMBL_6_proCap1 Procavia_capensis.proCap1.prediction_transcript Annotation source for Procavia_capensis prediction_transcript ENSEMBL_6_pteVam1 Pteropus_vampyrus.pteVam1.prediction_transcript Annotation source for Pteropus_vampyrus prediction_transcript ENSEMBL_6_tarSyr1 Tarsius_syrichta.tarSyr1.prediction_transcript Annotation source for Tarsius_syrichta prediction_transcript ENSEMBL_6_turTru1 Tursiops_truncatus.turTru1.prediction_transcript Annotation source for Tursiops_truncatus prediction_transcript ENSEMBL_6_vicPac1 Vicugna_pacos.vicPac1.prediction_transcript Annotation source for Vicugna_pacos prediction_transcript DS_667 hs36_clone Cloneset information from a NCBI36 assembly based Ensembl DS_668 8k_dkfz BAC array provided from Bernhard Radlwimmer and Peter Lichter from the DKFZ, Heidelberg, Germany (Anna Obenauf ticket 28160) DS_669 affy100k Affymetrix 100k (NCBI36) DS_670 affy10k Affymetrix 10k (NCBI36) DS_671 affy250_nsp affy250_nsp DS_672 affy500k Affymetrix 500k (NCBI36) DS_674 agilent_105a Agilent Human Genome CGH Microarray 105A (NCBI36) DS_675 agilent_human244 agilent_human244 DS_676 agilent_human44B agilent_human44B DS_678 agilent_human44A agilent_human44A DS_679 agilent_human185 agilent_human185 DS_683 BG_cytochip_v1_1 Bluegnome DS_684 BG_cytochip_v2_0 Bluegnome Provided by BlueGnome contact, David Chrimes - ticket 45502 Thu Sep 27 2007 DS_686 Eichler_36 Eichler cloneset( Oxford sent by Regina Regan (15/05/07)) mapped to NCBI 36 DS_692 ngrl_agilent Oligo array based on the Agilent 44b cloneset specific to the Wessex group (from Shuwen.Huang@salisbury) DS_693 nimblegen_hg18_wg Nimblegen Whole Genome (NCBI36) DS_694 spectral36 Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_697 ens_36_30k WTSI TPA (NCBI36 based on file:HuTP_IMF_NCBI36_02Feb07.cfg ) DS_698 ens_36_omimg OMIM morbidmap data mapped to NCBI36 assembly locations DS_699 ens_36_omim_genes OMIM genes mapped to NCBI 36 DS_700 hgnc36 HGNC mappings Mapping data from http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/gdlw.plHGNC HUGO DS_703 WGTP_regions_36 WGTP regions (redon et al) mapped to NCBI 36 DS_704 Cosmic_Protein_Mutation Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_708 Integr8 mRNA The Integr8 mRNA data source describes the coverage of protein sequences from the non-redundant sets available through Integr8 for each complete proteome by experimentally determined mRNA sequence. DS_709 Rfam Rfam DS_710 Community Annotation Annotations for regions in the zebrafish assembly Zv8 as reported by the community DS_717 CytoChip v3 CytoChip version 3 is a BAC based microarray designed for the investigation of genomic copy number imbalance associated with constitutional cytogenetic disorders. Please contact info@cambridgebluegnome.com for further information or with any questions. DS_719 NIDB Rat CNVs Rat Copy Number Variations, supplied by the Netherlands Institute for Developmental Biology. DS_721 MeDIP-seq Sperm DNA methylation landscape for Sperm, assayed using methyl DNA immunoprecipitation (MeDIP), Illumina Genome Analyzer sequencing and Bayesian Tool for Methylation Analysis (Batman). DS_722 EMMA European Mouse Mutant Archive (EMMA) DS_723 CHORI29 clones CHORI-29 NOD BAC Library, mapped to the NCBIM37 mouse assembly. The NOD/ShiLtJ mouse BAC library end-sequences have been mapped to the NCBIM37 mouse assembly using SSAHA alignment of the reads. DS_724 DIL NOD clones DIL NOD BAC Library, mapped to the NCBIM37 mouse assembly. The NOD/MrkTac mouse BAC library end-sequences have been mapped to the NCBIM37 mouse assembly using SSAHA alignment of the reads. DS_761 Ancora: Human-Zebrafish HCNEs Human non-exonic genomic regions conserved in the zebrafish (Danio rerio) genome. Minimum 70% identity over 50 alignment columns. More sources are available at http://ancora.genereg.net/das DS_762 Gene3D-CATH Domain Assignments to Ensembl CATH structural domains identified in Ensembl genomes using HMMs. Matches provided by Gene3D. DS_763 VectorBase Expression Simple summaries of microarray-based gene expression from VectorBase DS_764 Exome Full Set Full coverage exome coordinates set DS_765 ens_m37_129AB22 129S7/AB2.2 Clones DS_766 GO literature Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) generated from literature DS_767 disease literature Associated diseases for proteins in the UniProt Knowledgebase (UniProtKB) generated from literature DS_769 Bgee Bgee is a database to retrieve and compare gene expression patterns between animal species. DS_770 Prosite Full Alignments Retrieve the full sequence alignments for a PROSITE entry DS_771 EMAGE Mouse Embryo Spatial-Temporal In-Situ Gene Expression Resource DS_772 Vega genes Mapping of Vega genes to Ensembl DS_773 Vega genes Mapping of Vega genes to Ensembl DS_774 GRC region for Mouse assembly NCBIM_37 Region reported to the Genome Reference Consortium DS_775 GRC region NCBI_37 Region reported to the Genome Reference Consortium GRCh37 DS_817 Prosite Features (matches) The Prosite Feature DAS service provides features (Prosite matches, including level -1 not shown in UniProtKB. n.b. prosite rule derived sub-features are not shown. n.b. to get all features of a UniProtKB entry use the UniProtKB DAS service), sequence and type capabilities. DS_818 Zv_8 ZF-MODELS CLGY_Enhancer_Detection A DAS source that provides the insertions from the ZF-MODELS enhancer detection mutagenesis mapped to Zv_8 VEGA_3_Ggor_VEGA-clone Gorilla_gorilla.VEGA-clone.transcript Annotation source (returns clones) for Gorilla_gorilla transcript VEGA_4_Ggor_VEGA-clone Gorilla_gorilla.VEGA-clone.translation Annotation source (returns clones) for Gorilla_gorilla translation VEGA_3_Meug_VEGA-clone Macropus_eugenii.VEGA-clone.transcript Annotation source (returns clones) for Macropus_eugenii transcript VEGA_4_Meug_VEGA-clone Macropus_eugenii.VEGA-clone.translation Annotation source (returns clones) for Macropus_eugenii translation DS_823 IntOGen IntOGen is a resource that integrates multidimensional OncoGenomics Data for the identification of genes involved in development of different cancer types. DS_824 Ensembl genes Mapping of Ensembl genes to Vega DS_825 MGP_129P2_SNPs Mouse Genomes Project coding SNPs for strain 129P2; non-synonymous SNPs are in yellow, synonymous are in green. DS_826 MGP_129S1_SvImJ_SNPs Mouse Genomes Project coding SNPs for strain 129S1/SvImJ; non-synonymous SNPs are in yellow, synonymous are in green. DS_827 MGP_A_J_SNPs Mouse Genomes Project coding SNPs for strain A/J; non-synonymous SNPs are in yellow, synonymous are in green. DS_828 MGP_AKR_J_SNPs Mouse Genomes Project coding SNPs for strain AKR/J; non-synonymous SNPs are in yellow, synonymous are in green. DS_829 MGP_BALB_cJ_SNPs Mouse Genomes Project coding SNPs for strain BALB/cJ; non-synonymous SNPs are in yellow, synonymous are in green. DS_830 MGP_C3H_HeJ_SNPs Mouse Genomes Project coding SNPs for strain C3H/HeJ; non-synonymous SNPs are in yellow, synonymous are in green. DS_831 MGP_C57BL_6NJ_SNPs Mouse Genomes Project coding SNPs for strain C57BL/6NJ; non-synonymous SNPs are in yellow, synonymous are in green. DS_832 MGP_CAST_EiJ_SNPs Mouse Genomes Project coding SNPs for strain CAST/EiJ; non-synonymous SNPs are in yellow, synonymous are in green. DS_833 MGP_CBA_J_SNPs Mouse Genomes Project coding SNPs for strain CBA/J; non-synonymous SNPs are in yellow, synonymous are in green. DS_834 MGP_DBA_2J_SNPs Mouse Genomes Project coding SNPs for strain DBA/2J; non-synonymous SNPs are in yellow, synonymous are in green. DS_835 MGP_LP_J_SNPs Mouse Genomes Project coding SNPs for strain LP/J; non-synonymous SNPs are in yellow, synonymous are in green. DS_836 MGP_NOD_ShiLtJ_SNPs Mouse Genomes Project coding SNPs for strain NOD/ShiLtJ; non-synonymous SNPs are in yellow, synonymous are in green. DS_837 MGP_NZO_HiLtJ_SNPs Mouse Genomes Project coding SNPs for strain NZO/HiLtJ; non-synonymous SNPs are in yellow, synonymous are in green. DS_838 MGP_PWK_PhJ_SNPs Mouse Genomes Project coding SNPs for strain PWK/PhJ; non-synonymous SNPs are in yellow, synonymous are in green. DS_839 MGP_Spretus_EiJ_SNPs Mouse Genomes Project coding SNPs for strain Spretus/EiJ; non-synonymous SNPs are in yellow, synonymous are in green. DS_840 MGP_WSB_EiJ_SNPs Mouse Genomes Project coding SNPs for strain WSB/EiJ; non-synonymous SNPs are in yellow, synonymous are in green. DS_857 RNASeq An. gambiae (Gibbons et al.) This DAS source is the result of the alignments of Solexa reads from a next-generation sequencing study of the transcriptome by Gibbons and colleagues (doi:10.1093/molbev/msp188) focusing on Anopheles and Aedes. This DAS source returns the density of aligned reads per base. DS_858 RNASeq Ae. aegypti (Gibbons et al.) This DAS source is the result of the alignments of Solexa reads from a next-generation sequencing study of the transcriptome by Gibbons and colleagues (doi:10.1093/molbev/msp188) focusing on Anopheles and Aedes. This DAS source returns the density of aligned reads per base. DS_859 FireDB Functionally important residues from proteins with known structure DS_860 pdbchainfeatures Provides various third party annotations that have been computed for PDB chains. DS_861 pdb_uniprot_mapping Provides a DAS source that is serving the alignment between UniProtKB and PDB, derived from the SIFTS mappings. DS_863 go_hsa/bioinfo.cipf null DS_864 SNPedia DAS source mirroring data from SNPedia. SNPedia is a wiki investigating human genetics. We share information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA. DS_865 Cosmic Mutations in COLO-829 All genomic mutations in cellline COLO-829 from Cosmic DS_866 cbs_sort The combined result af the signalp, secretomep, targetp, netnes & lipop server for the given id DS_867 cbs_total The combined result of all of CBS DAS servers on the requested id DS_868 netacet NetAcet 1.0 server predicts substrates of N-acetyltransferase A (NatA) on yeast. DS_869 netnglyc The NetNglyc server predicts N-Glycosylation sites in human protein DS_870 netoglyc The NetOglyc server produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins DS_871 targetp TargetP predicts the subcellular location of eukaryotic proteins DS_872 tmhmm Prediction of transmembrane helices in proteins DS_873 ens_m37_bacmap BAC Clones (RP23/24 libraries) DAS Source For M37 C57BL/6J Mouse Assembly: End read sequences have been mapped to the M37 Mouse assembly using SSAHA. Clones positioned by appropriate read end pairs are indictated by black rectangles. Fingerprinting maps allow the positioning of extra clones (using map2gp). These are indicated by gold rectangles with black outlines. These may be associated (depicted with horizontal line) with single SSAHA mapped read ends (which are depicted as narrower black rectangles). DS_876 Test 1.6 sources Test for DAS 1.6 sources DS_877 Cosmic Mutations in NCI-H209 All genomic mutations in cellline NCI-H209 from Cosmic DS_918 Gasterosteus aculeatus 59_1l (all transcripts) SUPERFAMILY domain annotation for Gasterosteus aculeatus 59_1l (all transcripts). DS_919 Gallus gallus 59_2o (all transcripts) SUPERFAMILY domain annotation for Gallus gallus 59_2o (all transcripts). DS_920 Macaca mulatta 59_10n (all transcripts) SUPERFAMILY domain annotation for Macaca mulatta 59_10n (all transcripts). DS_921 Pongo pygmaeus 59_1e (all transcripts) SUPERFAMILY domain annotation for Pongo pygmaeus 59_1e (all transcripts). DS_922 Loxodonta africana 59_3b (all transcripts) SUPERFAMILY domain annotation for Loxodonta africana 59_3b (all transcripts). DS_923 Dasypus novemcinctus 59_2c (all transcripts) SUPERFAMILY domain annotation for Dasypus novemcinctus 59_2c (all transcripts). DS_924 Tursiops truncatus 59_1e (all transcripts) SUPERFAMILY domain annotation for Tursiops truncatus 59_1e (all transcripts). DS_925 Sus scrofa 59_9c (all transcripts) SUPERFAMILY domain annotation for Sus scrofa 59_9c (all transcripts). DS_926 Ornithorhynchus anatinus 59_1m (all transcripts) SUPERFAMILY domain annotation for Ornithorhynchus anatinus 59_1m (all transcripts). DS_927 Monodelphis domestica 59_5k (all transcripts) SUPERFAMILY domain annotation for Monodelphis domestica 59_5k (all transcripts). DS_928 Aedes aegypti 55 (all transcripts) SUPERFAMILY domain annotation for Aedes aegypti 55 (all transcripts). DS_929 Ochotona princeps 59_1e (all transcripts) SUPERFAMILY domain annotation for Ochotona princeps 59_1e (all transcripts). DS_930 Drosophila melanogaster 59_525a (all transcripts) SUPERFAMILY domain annotation for Drosophila melanogaster 59_525a (all transcripts). DS_931 Echinops telfairi 59_1i (all transcripts) SUPERFAMILY domain annotation for Echinops telfairi 59_1i (all transcripts). DS_932 Erinaceus europaeus 59_1g (all transcripts) SUPERFAMILY domain annotation for Erinaceus europaeus 59_1g (all transcripts). DS_933 Tetraodon nigroviridis 59_8d (all transcripts) SUPERFAMILY domain annotation for Tetraodon nigroviridis 59_8d (all transcripts). DS_934 Myotis lucifugus 59_1i (all transcripts) SUPERFAMILY domain annotation for Myotis lucifugus 59_1i (all transcripts). DS_935 Tupaia belangeri 59_1h (all transcripts) SUPERFAMILY domain annotation for Tupaia belangeri 59_1h (all transcripts). DS_936 Dipodomys ordii 59_1e (all transcripts) SUPERFAMILY domain annotation for Dipodomys ordii 59_1e (all transcripts). DS_937 Tarsius syrichta 59_1e (all transcripts) SUPERFAMILY domain annotation for Tarsius syrichta 59_1e (all transcripts). DS_938 Equus caballus 59_2f (all transcripts) SUPERFAMILY domain annotation for Equus caballus 59_2f (all transcripts). DS_939 Felis catus 59_1h (all transcripts) SUPERFAMILY domain annotation for Felis catus 59_1h (all transcripts). DS_940 Gorilla gorilla 59_3b (all transcripts) SUPERFAMILY domain annotation for Gorilla gorilla 59_3b (all transcripts). DS_941 Anopheles gambiae 49_3j (all transcripts) SUPERFAMILY domain annotation for Anopheles gambiae 49_3j (all transcripts). DS_942 Pteropus vampyrus 59_1e (all transcripts) SUPERFAMILY domain annotation for Pteropus vampyrus 59_1e (all transcripts). DS_943 Saccharomyces cerevisiae 59_2a (all transcripts) SUPERFAMILY domain annotation for Saccharomyces cerevisiae 59_2a (all transcripts). DS_944 Microcebus murinus 59_1d (all transcripts) SUPERFAMILY domain annotation for Microcebus murinus 59_1d (all transcripts). DS_945 Mus musculus 59 (all transcripts) SUPERFAMILY domain annotation for Mus musculus 59 (all transcripts). DS_946 Procavia capensis 59_1e (all transcripts) SUPERFAMILY domain annotation for Procavia capensis 59_1e (all transcripts). DS_947 Oryctolagus cuniculus 59_2b (all transcripts) SUPERFAMILY domain annotation for Oryctolagus cuniculus 59_2b (all transcripts). DS_948 Oryzias latipes 59_1k (all transcripts) SUPERFAMILY domain annotation for Oryzias latipes 59_1k (all transcripts). DS_949 Rattus norvegicus 59_34a (all transcripts) SUPERFAMILY domain annotation for Rattus norvegicus 59_34a (all transcripts). DS_950 Otolemur garnettii 59_1g (all transcripts) SUPERFAMILY domain annotation for Otolemur garnettii 59_1g (all transcripts). DS_951 Ciona intestinalis 59_2o (all transcripts) SUPERFAMILY domain annotation for Ciona intestinalis 59_2o (all transcripts). DS_952 Bos taurus 59_4h (all transcripts) SUPERFAMILY domain annotation for Bos taurus 59_4h (all transcripts). DS_953 Macropus eugenii 59_1b (all transcripts) SUPERFAMILY domain annotation for Macropus eugenii 59_1b (all transcripts). DS_954 Sorex araneus 59_1g (all transcripts) SUPERFAMILY domain annotation for Sorex araneus 59_1g (all transcripts). DS_955 Pan troglodytes 59_21n (all transcripts) SUPERFAMILY domain annotation for Pan troglodytes 59_21n (all transcripts). DS_956 Danio rerio 59_8e (all transcripts) SUPERFAMILY domain annotation for Danio rerio 59_8e (all transcripts). DS_957 Ciona savignyi 59_2j (all transcripts) SUPERFAMILY domain annotation for Ciona savignyi 59_2j (all transcripts). DS_958 Spermophilus tridecemlineatus 59_1i (all transcrip SUPERFAMILY domain annotation for Spermophilus tridecemlineatus 59_1i (all transcripts). DS_960 Callithrix jacchus 59_321a (all transcripts) SUPERFAMILY domain annotation for Callithrix jacchus 59_321a (all transcripts). DS_961 Cavia porcellus 59_3c (all transcripts) SUPERFAMILY domain annotation for Cavia porcellus 59_3c (all transcripts). DS_962 Canis familiaris 59_2o (all transcripts) SUPERFAMILY domain annotation for Canis familiaris 59_2o (all transcripts). DS_963 Caenorhabditis elegans 59_210a (all transcripts) SUPERFAMILY domain annotation for Caenorhabditis elegans 59_210a (all transcripts). DS_964 Vicugna pacos 59_1e (all transcripts) SUPERFAMILY domain annotation for Vicugna pacos 59_1e (all transcripts). DS_965 Xenopus tropicalis 59_41p (all transcripts) SUPERFAMILY domain annotation for Xenopus tropicalis 59_41p (all transcripts). DS_966 Homo sapiens 59_37d (all transcripts) SUPERFAMILY domain annotation for Homo sapiens 59_37d (all transcripts). DS_967 Anolis carolinensis 59_1c (all transcripts) SUPERFAMILY domain annotation for Anolis carolinensis 59_1c (all transcripts). DS_1028 InterPro-Matches-Overview Shows the maximum extent of the matches from all signatures that are integrated into a single InterPro entry against UniProtKB protein sequences (i.e. if an InterPro entry contains 2 signatures, A and B, and both of these match a protein, A between residue 3 and 125 and B between residue 5 and 127, the overview supermatch of these signatures is between 3 and 127). DS_1029 InterPro-UniParc-matches Contains all InterPro member database signature matches to all UniParc protein sequences. ENSEMBL_4_GRCh37 Homo_sapiens.GRCh37.translation Annotation source for Homo_sapiens translation DS_1254 PeptideAtlas Mouse Information exported from PeptideAtlas Mouse build. DS_1255 PeptideAtlas Human Information exported from PeptideAtlas Human build. DS_1256 PeptideAtlas Drosophila Peptides information exported from PeptideAtlas Drosophila build. DS_1257 PeptideAtlas Yeast Peptides from the PeptideAtlas Yeast build DS_1258 PeptideAtlas Yeast MRM Peptides from the PeptideAtlas Yeast MRM PeptideAtlas build DS_1259 PeptideAtlas Human Plasma Peptides from the PeptideAtlas Human Plasma build DS_1260 PeptideAtlas Human Urine Peptides from the PeptideAtlas Human Urine build DS_1261 PeptideAtlas Mouse Plasma Peptides from the PeptideAtlas Mouse Plasma build DS_1262 Meleagris gallopavo 57_2 (all transcripts) SUPERFAMILY domain annotation for Meleagris gallopavo 57_2 (all transcripts). DS_1263 Taeniopygia guttata 59_1e (all transcripts) SUPERFAMILY domain annotation for Taeniopygia guttata 59_1e (all transcripts). DS_1289 PhenCode PhenCode connects human phenotype and clinical data in various locus-specific mutation databases (LSDBs) with data on genome sequences, evolutionary history, and function in genome browsers. DS_1290 ArkDB Chick Markers ePCR mapping of Chicken Markers found at www.thearkdb.org.uk on to the WASHUC_2 assembly DS_1291 ArkBD Pig Markers ePCR mappings of pig markers found at www.thearkdb.org.uk on to the Sscrofa9 Pig genome assembly DS_1292 ArkDB Cow Markers ePCR mappings of cow markers found at www.thearkdb.org.uk on to the cow btau4.0 genome assembly DS_1293 ArkDB Turkey Markers ePCR mappings of turkey markers found at www.thearkdb.org.uk on to the turkey UMD2 genome assembly DS_1294 Anopheles albimanus ESTs Around 3200 ESTs/EST clusters from Anopheles albimanus have been aligned to the AgamP3 genome assembly (Anopheles gambiae). DS_1295 Mass spec. proteomics (JHU II) We carried out a comprehensive mass spectrometry analysis of midgut, salivary gland and ovary of adult female mosquito using LTQ Orbitrap XL ETD high resolution mass spectrometer. We analyzed the mass spectrometry derived data in Mascot search algorithm using six frame translation of genome and protein database of Anopheles, Aedes and Drosophila. We identified novel genes, corrected and validated gene annotations of Anopheles gambiae. DS_1296 "NextGen" Expression Interim handling of VEGA_7_Cfam_VEGA Canis_familiaris.VEGA.prediction_transcript Annotation source for Canis_familiaris prediction_transcript VEGA_1_Cfam_VEGA Canis_familiaris.VEGA.reference Canis_familiaris Reference server based on VEGA assembly. Contains 1 top level entries. VEGA_3_Cfam_VEGA Canis_familiaris.VEGA.transcript Annotation source for Canis_familiaris transcript VEGA_4_Cfam_VEGA Canis_familiaris.VEGA.translation Annotation source for Canis_familiaris translation VEGA_7_Ggor_VEGA Gorilla_gorilla.VEGA.prediction_transcript Annotation source for Gorilla_gorilla prediction_transcript VEGA_1_Ggor_VEGA Gorilla_gorilla.VEGA.reference Gorilla_gorilla Reference server based on VEGA assembly. Contains 2 top level entries. VEGA_3_Ggor_VEGA Gorilla_gorilla.VEGA.transcript Annotation source for Gorilla_gorilla transcript VEGA_4_Ggor_VEGA Gorilla_gorilla.VEGA.translation Annotation source for Gorilla_gorilla translation VEGA_7_Meug_VEGA Macropus_eugenii.VEGA.prediction_transcript Annotation source for Macropus_eugenii prediction_transcript VEGA_1_Meug_VEGA Macropus_eugenii.VEGA.reference Macropus_eugenii Reference server based on VEGA assembly. Contains 1 top level entries. VEGA_3_Meug_VEGA Macropus_eugenii.VEGA.transcript Annotation source for Macropus_eugenii transcript VEGA_4_Meug_VEGA Macropus_eugenii.VEGA.translation Annotation source for Macropus_eugenii translation VEGA_2_Sscr_VEGA Sus_scrofa.VEGA.karyotype Annotation source for Sus_scrofa karyotype VEGA_7_Sscr_VEGA Sus_scrofa.VEGA.prediction_transcript Annotation source for Sus_scrofa prediction_transcript VEGA_1_Sscr_VEGA Sus_scrofa.VEGA.reference Sus_scrofa Reference server based on VEGA assembly. Contains 3 top level entries. VEGA_3_Sscr_VEGA Sus_scrofa.VEGA.transcript Annotation source for Sus_scrofa transcript VEGA_4_Sscr_VEGA Sus_scrofa.VEGA.translation Annotation source for Sus_scrofa translation UCSC_hg19 hg19 Human Feb. 2009 (GRCh37/hg19) Genome at UCSC Note: this source should be used with a type filter on the end of a features request e.g. &type=bacEndPairs&type=ensGene UCSC_hg18 hg18 Human Mar. 2006 (NCBI36/hg18) Genome at UCSC Note: this source should be used with a type filter on the end of a features request e.g. &type=bacEndPairs&type=ensGene UCSC_hg17 hg17 Human May 2004 (NCBI35/hg17) Genome at UCSC Note: this source should be used with a type filter on the end of a features request e.g. &type=bacEndPairs&type=ensGene UCSC_hg16 hg16 Human July 2003 (NCBI34/hg16) Genome at UCSC Note: this source should be used with a type filter on the end of a features request e.g. &type=bacEndPairs&type=ensGene UCSC_mm9 mm9 Mouse July 2007 (NCBI37/mm9) Genome at UCSC Note: this source should be used with a type filter on the end of a features request e.g. &type=bacEndPairs&type=ensGene UCSC_mm8 mm8 Mouse Feb. 2006 (NCBI36/mm8) Genome at UCSC Note: this source should be used with a type filter on the end of a features request e.g. &type=bacEndPairs&type=ensGene UCSC_mm7 mm7 Mouse Aug. 2005 (NCBI35/mm7) Genome at UCSC Note: this source should be used with a type filter on the end of a features request e.g. &type=bacEndPairs&type=ensGene UCSC_cavPor3 cavPor3 Guinea pig Feb. 2008 (Broad/cavPor3) Genome at UCSC Note: this source should be used with a type filter on the end of a features request e.g. &type=bacEndPairs&type=ensGene UCSC_equCab2 equCab2 Horse Sep. 2007 (Broad/equCab2) Genome at UCSC Note: this source should be used with a type filter on the end of a features request e.g. &type=bacEndPairs&type=ensGene UCSC_susScr2 susScr2 Pig Nov. 2009 (SGSC Sscrofa9.2/susScr2) Genome at UCSC Note: this source should be used with a type filter on the end of a features request e.g. &type=bacEndPairs&type=ensGene UCSC_loxAfr3 loxAfr3 Elephant Jul. 2009 (Broad/loxAfr3) Genome at UCSC Note: this source should be used with a type filter on the end of a features request e.g. &type=bacEndPairs&type=ensGene UCSC_anoCar1 anoCar1 Lizard Feb. 2007 (Broad/anoCar1) Genome at UCSC Note: this source should be used with a type filter on the end of a features request e.g. &type=bacEndPairs&type=ensGene UCSC_oryLat2 oryLat2 Medaka Oct. 2005 (NIG/UT MEDAKA1/oryLat2) Genome at UCSC Note: this source should be used with a type filter on the end of a features request e.g. &type=bacEndPairs&type=ensGene UCSC_dm3 dm3 D. melanogaster Apr. 2006 (BDGP R5/dm3) Genome at UCSC Note: this source should be used with a type filter on the end of a features request e.g. &type=bacEndPairs&type=ensGene UCSC_dm2 dm2 D. melanogaster Apr. 2004 (BDGP R4/dm2) Genome at UCSC Note: this source should be used with a type filter on the end of a features request e.g. &type=bacEndPairs&type=ensGene UCSC_dm1 dm1 D. melanogaster Jan. 2003 (BDGP R3/dm1) Genome at UCSC Note: this source should be used with a type filter on the end of a features request e.g. &type=bacEndPairs&type=ensGene DS_1413 60k_SNP 60K SNPs project. SNPs mapped with flanking sequence onto the Pig genome ver 9. Only unique mapping are displayed. DS_1415 cnio_massspec Human mass-spec peptides mapped to Gencode 3c by M.Tress et al., CNIO DS_1416 Cosmic Transcripts Transcripts from Cosmic mapped to Human GRCh 37 DS_1417 Cosmic Mutations Mutations from Cosmic mapped to Human GRCh 37 DS_1418 Cosmic Mutations in COLO-829 All genomic mutations in cellline COLO-829 from Cosmic DS_1419 Cosmic Mutations in NCI-H209 All genomic mutations in cellline NCI-H209 from Cosmic DS_1420 uniprot2probes Annotation source with microarray probes mapping uniprot sequences. DS_1436 Pride DAS 1.6 Pride DAS source updated to 1.6 version of DAS DS_1523 hsa_54_36p Human genome annotation from Ensembl 54 (via biojava-ensembl) DS_1524 hsa_59_37d Human genome annotation from Ensembl 59 via biojava-ensembl (gene structures are GENCODE 4) DS_1525 medipseq_reads MeDIP-seq read mappings from Nature Biotech. 26:779-785 DS_1526 uniprot_exon_snp Ensembl exon boundary and SNP data projected on UniProt sequence. Based on the COMPARA ENSP-UniProt mapping. DS_1527 demo_histo shows score from signal peptide prediction DS_1528 demo_gradient shows score from signal peptide prediction DS_1529 demo_lineplot shows score from signal peptide prediction DS_1530 demo_nostyle shows score from signal peptide prediction DS_1531 yale_pseudogenes pseudogenes coming from Philip at Yale. DS_1532 DECIPHER_HGNC HGNC mappings Mapping data from http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/gdlw.pl HGNC HUGO DS_1533 Human CCDS Public Note CCDS Public Note DS_1534 Mouse CCDS Public Note CCDS Public Note DS_1535 decipher DECIPHER V5.1 DS_1536 segdup_washu_36_collapsed segdup_washu_36_collapsed DS_1537 desmith DeSmith(http://projects.tcag.ca/variation/downloads/deSmith2007.txt) DS_1540 agilent_4x44 agilent_4x44 DS_1542 WGTP_loci_36 WGTP regions (redon et al) mapped to NCBI 36 DS_1544 ens5236ngenes ens5236ngenes DS_1552 x_chromosome_tiling_array X-chromosome Tiling array (Leuven: 22/10/07) DS_1553 xhd xhd DS_1554 xes xes DS_1555 s+vt s+vt DS_1556 sanger244kv2 sanger244kv2 DS_1557 toronto_poly_36 Database of Genetic Variations DAS Source For NCBI36 Human Assembly (hg18): The Database of Genomic Variants is a curated catalogue of large-scale variation in the human genome.The data displayed was obtained from their download site (which was last updated here on 31st July 2008). There are 59 Inversion, 6481 CopyNumber and 18 InversionBreakpoint features. DS_1558 iPfamInteraction iPfamLigInteraction das source offers the ligands interactions with the pfam domain. DS_1559 ens_36_segdup_washu ens_36_segdup_washu DS_1560 KO_designs Recombineering oligos for knockout designs (Sanger HTGT). DS_1561 KO_designs_cr Candidate regions for knockout designs (Sanger HTGT). DS_1562 custom_KO_designs Recombineering oligos for custom knockout designs (Sanger HTGT). DS_1563 KO_vectors Recombineering oligos for constructed knockout designs (Sanger HTGT). DS_1564 mouse_KOs Orthologous_mouse_KOs DS_1565 ikmc_products IKMC - Knockout Mutant Mouse Alleles DS_1566 team87_production_constructs Recombineering oligos for knockout designs (Sanger HTGT). DS_1572 ens_zfish7_morpholino ens_zfish7_morpholino DS_1573 Havana manual annotation (GRCh37) A DAS source that provides access to the manual annotation data inside the Otter database in GRCh37 coordinates. DS_1574 Havana Pig manual annotations A DAS source that provides access to the manual annotation data inside the Otter database for Pig. DS_1575 ChromatinSigs TSS predictions based on combined chromatin signatures (Jason Ernst, MIT) DS_1576 CCDS human Human transcripts part of the CCDS set DS_1577 CCDS mouse Murine transcripts part of the CCDS set DS_1578 ASPIC ASPIC alternative isoforms on NCBI 36 DS_1579 important GENCODE issues Loci and transcripts flagged in the AnnoTrack system for the attention of annotators DS_1580 peptides confirmed by mass spectrometrometry A DAS source that provides access to the automatic annotation data from mass spectrometry (translational evidence) DS_1584 KO_mouse_genes Knockout mouse genes DS_1585 homo_sapiens_KO_mouse_orthologues Knockout mouse orthologues for homo sapiens DS_1586 danio_rerio_KO_mouse_orthologues Knockout mouse orthologues for zebrafish DS_1587 constrained_regions Regions of constrained elements outside of current GENCODE annotation from TFBS, RNA-Seq, open chromatin and other RNA data (supplied by ENCODE comparative group). ENCODE usage restrictions apply. DS_1588 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1589 BacAbs predictions for organisms studied by the BacAbs project DS_1590 hydroph hydroph DS_1591 KD_hydroph KD_hydroph DS_1592 BM_hydroph BM_hydroph DS_1593 metatm metatm DS_1594 MGI Representative Transcripts Mouse_37; MGI_Representative_Transcripts track; MGI Representative Transcripts; For all MGI gene and transcript tracks (i.e. not including ENSEMBL and NCBI gene models and the VEGA annotations) coordinates in the build 36 assembly were either downloaded from UCSC (mrnas, ests, refseq NM and NRs) or BLATted locally (tigr, DoTS, NIA, and refseq XM and XRs). Local BLAT results were filtered using pslReps -singleHit. These pools of coordinates were subsequently mined for relevant sequences based on various MGI database reports. Entries in the track are named using the GenBank sequence ID prepended to the MGI symbol. Each item in the track links to the corresponding MGI marker detail page. DS_1595 QTL Mouse_37; QTL track; QTL; Quantitative trait loci were mapped to the build 36 assembly based on the known location of the STS markers that define the peaks and flanks of the QTL. Each QTL entry in the track links to the corresponding MGI marker detail page. As most QTLs that have flank as well as peak data are far longer than the 1 Mbase GBrowse easily displays, the QTL track is also shown in a compressed form in the overview panel. DS_1596 Adipose_tissue Mouse_37; Adipose_tissue track; Adipose_tissue; Please see notes under MGI_Representative_Transcripts track for assembly and coordinate details. The MGI database report, MGI_PhenotypicAllele.rpt, was parsed for markers and alleles that are associated with transcripts (not including gene model transcripts) and the Top Level Mammalian Phenotype (MP) terms were captured. Note that these top level terms can be associated with a marker multiple times (i.e. via multiple alleles). A track for each of the top-level MP terms, were then created. Within each track, the intron-exon structure of the transcript representing that marker has been preserved in the display. Track entries are named with a catenation of seqID, marker symbol, and MP term. From the phenotypes tracks, each entry links to a page that summarizes the phenotypic/allele details. The Mammalian Phenotype Ontology can be browsed here. DS_1597 Behavior_neurological Mouse_37; Behavior_neurological track; Behavior_neurological; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1598 Cardiovascular_system Mouse_37; Cardiovascular_system track; Cardiovascular_system; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1599 Cellular Mouse_37; Cellular track; Cellular; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1600 Craniofacial Mouse_37; Craniofacial track; Craniofacial; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1601 Digestive_alimentary Mouse_37; Digestive_alimentary track; Digestive_alimentary; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1602 Embryogenesis Mouse_37; Embryogenesis track; Embryogenesis; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1603 Endocrine_exocrine_gland Mouse_37; Endocrine_exocrine_gland track; Endocrine_exocrine_gland; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1604 Growth_size Mouse_37; Growth_size track; Growth_size; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1605 Hearing_ear Mouse_37; Hearing_ear track; Hearing_ear; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1606 Hematopoietic_system Mouse_37; Hematopoietic_system track; Hematopoietic_system; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1607 Homeostasis_metabolism Mouse_37; Homeostasis_metabolism track; Homeostasis_metabolism; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1608 Immune_system Mouse_37; Immune_system track; Immune_system; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1609 Lethality-embryonic_perinatal Mouse_37; Lethality_embryonic_perinatal track; Lethality-embryonic_perinatal; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1610 Lethality-postnatal Mouse_37; Lethality_postnatal track; Lethality-postnatal; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1611 Life_span-post-weaning_aging Mouse_37; Life_span_post_weaning_aging track; Life_span-post-weaning_aging; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1612 Limbs_digits_tail Mouse_37; Limbs_digits_tail track; Limbs_digits_tail; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1613 Liver_biliary_system Mouse_37; Liver_biliary_system track; Liver_biliary_system; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1614 Muscle Mouse_37; Muscle track; Muscle; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1615 Nervous_system Mouse_37; Nervous_system track; Nervous_system; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1616 Pigmentation Mouse_37; Pigmentation track; Pigmentation; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1617 Renal_urinary_system Mouse_37; Renal_urinary_system track; Renal_urinary_system; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1618 Reproductive_system Mouse_37; Reproductive_system track; Reproductive_system; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1619 Respiratory_system Mouse_37; Respiratory_system track; Respiratory_system; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1620 Skeleton Mouse_37; Skeleton track; Skeleton; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1621 Skin_coat_nails Mouse_37; Skin_coat_nails track; Skin_coat_nails; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1622 Taste_olfaction Mouse_37; Taste_olfaction track; Taste_olfaction; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1623 Touch_vibrissae Mouse_37; Touch_vibrissae track; Touch_vibrissae; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1624 Tumorigenesis Mouse_37; Tumorigenesis track; Tumorigenesis; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1625 Vision_eye Mouse_37; Vision_eye track; Vision_eye; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1626 Normal_phenotype Mouse_37; Normal_phenotype track; Normal_phenotype; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1627 Other_phenotype Mouse_37; Other_phenotype track; Other_phenotype; Please see notes under Adipose_tissue track in phenotypes for phenotype details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1628 Alleles_induced Mouse_37; Alleles_induced track; Alleles_induced; Please see notes under Alleles_gene_trapped track in Alleles for allele details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1629 Alleles_spontaneous Mouse_37; Alleles_spontaneous track; Alleles_spontaneous; Please see notes under Alleles_gene_trapped track in Alleles for allele details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1630 Alleles_targeted Mouse_37; Alleles_targeted track; Alleles_targeted; Please see notes under Alleles_gene_trapped track in Alleles for allele details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1631 Alleles_transgenic Mouse_37; Alleles_transgenic track; Alleles_transgenic; Please see notes under Alleles_gene_trapped track in Alleles for allele details and notes under MGI_Representative_Transcripts track for assembly and coordinate details DS_1632 GeneTraps_per_Gene Mouse_37; GeneTraps_per_gene track; GeneTraps_per_Gene; Color-coded gene trap frequency track for MGI genes, indicating the number of gene trap insertions per gene. Only gene trap insertions that "trap" a gene (i.e., overlap the gene's coordinates in the correct transcriptional orientation) are counted. If gene model colored red there are >1000 gene traps associated with the gene, orange is 101 to 1000, green is 11 to 100, blue is 2 to 10, violet is just a single genetrap, and black is no gene traps associated with the gene. DS_1633 GeneTraps_RNA_tags Mouse_37; MGI_RNA_Gtraps track; GeneTraps_RNA_tags; Gene Trap sequence tags from GenBank dbGSS that have an RNA-based sequence tag method (5'-RACE or 3'-RACE). RNA-based gene trap sequence tags are derived from the exon adjacent to the insertion site. If the sequence tag method is 5'-RACE (blue), the insertion site is in the intron downstream from the most 3' exon represented in the sequence tag. If the sequence tag is 3'-RACE (green), the insertion site is in the intron upstream from the most 5' exon represented in the sequence tag. Gene trap mutagenesis requires that the vector inserts in the correct transcriptional orientation of the "trapped" gene. Sequence tags that overlap known genes in the opposite transcriptional orientation do not disrupt those genes from a gene trapping mechanism, and are not counted in the GeneTraps_per_Gene track. DS_1634 asd_gene [GeneView] AltSplice features on human and mouse genes. DS_1635 atd_gene [GeneView] AltTrans features on human and mouse genes. DS_1636 NASC (fei_0) Variants from the European Arabidopsis Stock Centre DS_1637 asd_snp_mouse [ContigView] SNPs on AltSplice mouse alternative splicing patterns. DS_1638 atd_mouse [ContigView] AltTrans mouse alternative transcript patterns. DS_1639 NASC (van_0) Variants from the European Arabidopsis Stock Centre DS_1640 NASC (c24) Variants from the European Arabidopsis Stock Centre DS_1641 NASC (bay_0) Variants from the European Arabidopsis Stock Centre DS_1642 asd_snp_human [ContigView] SNPs on AltSplice human alternative splicing patterns. DS_1643 NASC (tamm_2) Variants from the European Arabidopsis Stock Centre DS_1644 NASC (got_7) Variants from the European Arabidopsis Stock Centre DS_1645 asd_human [ContigView] AltSplice human alternative splicing patterns. DS_1646 NASC (tsu_1) Variants from the European Arabidopsis Stock Centre DS_1647 NASC (nfa_8) Variants from the European Arabidopsis Stock Centre DS_1648 JHU MS [Anopheles gambiae] MS data from Pandey lab, JHU DS_1649 atd_human [ContigView] AltTrans human alternative transcript patterns. DS_1650 Transposons [Anopheles gambiae] Transposons annotated on chromosome coordinates. DS_1651 NASC (lov_5) Variants from the European Arabidopsis Stock Centre DS_1652 NASC (bur_0) Variants from the European Arabidopsis Stock Centre DS_1653 NASC (br_0) Variants from the European Arabidopsis Stock Centre DS_1654 NASC (ler_1) Variants from the European Arabidopsis Stock Centre DS_1655 asd_mouse [ContigView] AltSplice mouse alternative splicing patterns. DS_1656 NASC (ts_1) Variants from the European Arabidopsis Stock Centre DS_1657 NASC (est_1) Variants from the European Arabidopsis Stock Centre DS_1658 NASC (rrs_7) Variants from the European Arabidopsis Stock Centre DS_1659 NASC (shakhdara) Variants from the European Arabidopsis Stock Centre DS_1660 NASC (bor_4) Variants from the European Arabidopsis Stock Centre DS_1661 NASC (rrs_10) Variants from the European Arabidopsis Stock Centre DS_1662 NASC (cvi_0) Variants from the European Arabidopsis Stock Centre DS_1663 citexplore_split The top citations for a PDB ID, Uniprot Accession or gene name, sourced from CiteXplore. DS_1664 Top Selective Sweep Regions DAS source providing coordinates of the regions with the z-scores amongst the smallest 5% of all regions identified by Selective Sweep Scan DS_1665 Catalog of Changes DAS source providing Neandertal alleles for positions of non-synonymous difference between human and chimpanzee DS_1666 Selective Sweep Error DAS source providing the standard error for corresponding z-scores from the Selective Sweep Scan DS_1667 Selective Sweep Z-scores DAS source providing z-scores from the Selective Sweep Scan DS_1668 PDBe Summary Basic summary data for PDB structures. DS_1669 phdsec phdsec DS_1670 toppred toppred DS_1671 phdacc phdacc DS_1672 signalp signalp DS_1673 phdhtm phdhtm DS_1674 phobius phobius DS_1675 hmmtop hmmtop DS_1948 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1949 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1950 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1951 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1952 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1953 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1954 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1955 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1956 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1957 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1958 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1959 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1960 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1961 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1962 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1963 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1964 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1965 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1966 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1967 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1968 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1969 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1970 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1971 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1972 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1973 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1974 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1975 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1976 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1977 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1978 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1979 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1980 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1981 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1982 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1983 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1984 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1985 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1986 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1987 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1988 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1989 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1990 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1991 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1992 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1993 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1994 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1995 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_1996 pubmed2ensembl www.pubmed2ensembl.org -- linking publications and genes DS_2058 IKMC_Trapped_Alleles IKMC Trapped Alleles DS_2059 hs35_clone Cloneset information from a NCBI35 assembly based Ensembl DS_2060 spectral34 Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2061 ens_36_imprinted_genes Imprinted genes (Otago website) mapped to NCBI 36 DS_2063 ens_m35_genetrap Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2064 ens_m36_genetrap GeneTrap DAS Source For M36 Mouse Assembly: GeneTrap sequence tags generated by the International Gene Trap Consortium and mapped to the NCBI m36 mouse assembly. DS_2065 ens3335genes Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2066 ens_ncbi_35_morbid Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2067 pigends_all_humanNCBI35 Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2068 pigends_all_humanNCBI36 Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2069 snp_Zv4 Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2070 indel_Zv4 Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2071 snp_Zv5 Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2072 indel_Zv5 Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2073 ens_36_exoseq_sts STS designed to amplify and sequence exons in the ExoSeq SNP detection program (NCBI36 coordinates). DS_2074 ens_35_compugen Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2075 ens_36_compugen Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2076 ens_m33_compugen Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2077 ens_rat34_compugen Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2078 ens_rat34_bacend Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2079 ens_35_toronto_dbgv Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2080 ens_35_genexref Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2081 ens_m33_genexref Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2082 ens_m33_nia_genes Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2083 ens_m33_mgi_pheno Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2084 ens_m34_129AB22 Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2085 ens_m35_129AB22 Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2086 ens_m36_129AB22 AB 2.2 Clones DAS Source For M36 Mouse Assembly: The end read sequences have been mapped to the M36 Mouse assembly using SSAHA. DS_2087 ens_m34_compugen Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2089 ens_m36_compugen Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2090 ens_m34_geneid Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2091 ens_m35_geneid Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2092 ens_m36_geneid geneid DAS Source For M36 Mouse Assembly: The geneid v1.2 gene predictions for the M36 Mouse assembly. DS_2093 ens_m34_sgp Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2094 ens_m35_sgp Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2095 ens_m36_sgp sgp DAS Source For M36 Mouse Assembly: The sgp gene predictions for the M36/ mm8 Mouse assembly. DS_2096 ens_m34_refseq Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2097 ens_m35_refseq Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2098 ens_m36_refseq NCBI RefSeq mappings to Mouse NCBIM36 C57BL/6J reference assembly DS_2099 ens_36_refseq NCBI RefSeq mappings to Human NCBI36 reference assembly DS_2100 ens_m34_nia_genes Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2101 ens_m35_nia_genes Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2102 ens_m36_nia_genes NIA Mouse Gene Index DS_2103 ens_m34_nod_clones Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2104 ens_m35_nod_clones Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2105 ens_m36_nod_clones NOD BAC Library DAS Source For M36 Mouse Assembly:The NOD/MrkTac Mouse BAC Library end sequences have been mapped to the M36 Mouse assembly using SSAHA. DS_2106 ens_m36_nodtiling NOD BAC MTP DAS Source For M36 Mouse Assembly: A subset of the NOD/MrkTac Mouse BAC Library, as mapped in the full DAS, representing a minimum tiling path (with 20K bp clone overlap). DS_2107 ens_m34_chori_clones Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2108 ens_m35_chori_clones Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2109 ens_m36_chori_clones CHORI-29 NOD BAC Library DAS Source For M36 Mouse Assembly: The CHORI-29 NOD Mouse BAC Library end sequences have been mapped to the M36 Mouse assembly using SSAHA. DS_2110 ens_m36_choritiling CHORI-29 NOD BAC MTP DAS Source For M36 Mouse Assembly: A subset of the CHORI-29 NOD Mouse BAC Library, as mapped in the full DAS, representing a minimum tiling path (with 20K bp clone overlap). DS_2111 ens_m35_c3h_bacs Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2112 ens_m36_c3h_bacs Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2113 ens_m34_micer Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2114 ens_m35_micer Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2115 ens_m36_micer MICER DAS Source For M36 Mouse Assembly: The http://www.sanger.ac.uk/PostGenomics/mousegenomics/ Mutagenic Insertion and Chromosome Engineering Resource (MICER) provides vectors for generating knockout mice, and for chromosome engineering. The end read sequences have been mapped to the M36 Mouse http://www.ncbi.nlm.nih.gov/genome/seq/NCBIContigInfo.html using http://www.sanger.ac.uk/Software/analysis/SSAHA/. The associated stylesheet suggest glyphs for the clones which match the colour and shape of those described in the paper Mutagenic insertion and chromosome engineering resource (MICER).Adams DJ, Biggs PJ, Cox T, Davies R, van der Weyden L, Jonkers J, Smith J, Plumb B, Taylor R, Nishijima I, Yu Y, Rogers J, Bradley A Nat Genet. 2004;36;867-71. PMID: 15235602 DS_2116 ens_m34_bac Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2117 ens_m34_bacmap Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2118 ens_m36_bacmap BAC Clones (RP23/24 libraries) DAS Source For M36 C57BL/6J Mouse Assembly: End read sequences have been mapped to the M36 Mouse assembly using SSAHA. Clones positioned by appropriate read end pairs are indictated by gold rectangles with black outlines. Fingerprinting maps allow the positioning of extra clones (using map2gp). These are indicated by gold rectangles without outlines. These may be associated (depicted with horizontal line) with single SSAHA mapped read ends (which are depicted as narrower black rectangles). DS_2119 ens_m34_msm Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2120 ens_m35_msm Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2121 ens_m36_msm MSM BAC Library DAS Source For M36 Mouse Assembly: The MSM Mouse BAC Library end sequences have been mapped to the M36 Mouse assembly using SSAHA. DS_2122 ens_m34_dots Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2123 ens_m34_mgc Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2124 ens_m35_mgc Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2125 ens_m36_mgc MGC DAS Source For M36 Mouse Assembly: Transcripts from full-length open reading frame (FL-ORF) clones provided by the Mammalian Gene Collection (MGC) mapped (by UCSC) to the M36 Mouse assembly. DS_2126 ens_m35_gnomon Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2127 ens_m36_gnomon NCBI Gnomon HMM predictions for Mouse NCBIM36 C57BL/6J reference assembly DS_2128 ens_36_gnomon NCBI Gnomon HMM predictions for Human NCBI36 reference assembly DS_2129 ens_35_hver Sanger Hver Array mapping to NCBI35 reference assembly DS_2130 ens_36_hver Sanger Hver Array mapping to NCBI36 reference assembly DS_2131 ens_35_horse Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2132 ens_35_cpg_clones Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2133 ens_36_cpg_clones CpG clones created using a methylated region bias selection technique mapped to the NCBI36 human assembly DS_2134 ens_36_cpg_eponine CpG predicitons by Eponine on NCBI36 human assembly DS_2143 ens_m34_1Mb_clones Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2144 ens_m34_0.5Mb_clones Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2145 ens_m36_1Mb_clones The C57BL/6J 1MB clone subset from the RP23/24 libraries. DS_2146 ens_m36_0.5Mb_clones The C57BL/6J 0.5MB clone subset from the RP23/24 libraries. DS_2147 ens_m37_1Mb_clones The C57BL/6J 1MB clone subset from the RP23/24 libraries. DS_2148 ens_m37_0.5Mb_clones The C57BL/6J 0.5MB clone subset from the RP23/24 libraries. DS_2150 ens_35_m2h Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2151 ens_35_m2h2 Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2152 ens_35_m2d2 Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2153 ens_35_m2m2 Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2154 ens_35_illumina Illumina probes mapped to NCBI35 Homo Sapiens assembly using SSAHA2 DS_2155 ens_36_illumina Illumina probes mapped to NCBI36 Homo Sapiens assembly using SSAHA2 DS_2156 ens_m34_illumina Illumina probes mapped to NCBIM34 Mus musculus assembly using SSAHA2 DS_2157 ens_m35_illumina Illumina probes mapped to NCBIM35 Mus musculus assembly using SSAHA2 DS_2158 ens_m36_illumina Illumina probes mapped to NCBIM36 Mus musculus assembly using SSAHA2 DS_2159 ens_m34_tilingpath_clones The C57BL/6J tiling path clone set from the RP23/24 libraries. DS_2160 ens_m35_tilingpath_clones The C57BL/6J tiling path clone set from the RP23/24 libraries. DS_2161 ens_m36_tilingpath_clones The C57BL/6J tiling path clone subset from the RP23/24 libraries. DS_2162 ens_m37_tilingpath_clones The C57BL/6J tiling path clone subset from the RP23/24 libraries. DS_2163 ens_35_COX_SNP SNPs formed when comparing the COX haplotype against PGF DS_2164 ens_35_COX_DIP DIPs formed when comparing the COX haplotype against PGF DS_2165 ens_35_QBL_SNP SNPs formed when comparing the QBL haplotype against PGF DS_2166 ens_35_QBL_DIP DIPs formed when comparing the QBL haplotype against PGF DS_2167 ens_35_APD_SNP SNPs formed when comparing the APD haplotype against PGF DS_2168 ens_35_APD_DIP DIPs formed when comparing the APD haplotype against PGF DS_2169 ens_35_DBB_SNP SNPs formed when comparing the DBB haplotype against PGF DS_2170 ens_35_DBB_DIP DIPs formed when comparing the DBB haplotype against PGF DS_2171 ens_35_MCF_SNP SNPs formed when comparing the MCF haplotype against PGF DS_2172 ens_35_MCF_DIP DIPs formed when comparing the MCF haplotype against PGF DS_2173 ens_35_MANN_SNP SNPs formed when comparing the MANN haplotype against PGF DS_2174 ens_35_MANN_DIP DIPs formed when comparing the MANN haplotype against PGF DS_2175 ens_35_SSTO_SNP SNPs formed when comparing the SSTO haplotype against PGF DS_2176 ens_35_SSTO_DIP DIPs formed when comparing the SSTO haplotype against PGF DS_2177 ens_35_operon Mapping of Operon primers to NCBI35 DS_2178 ens_m34_operon Mapping of Operon primers to NCBIM34 DS_2179 ens_m35_operon Mapping of Operon primers to NCBIM35 DS_2180 ens_36_fosmid Fosmids positioned by pairing SSAHA2 alignments of their sequence ends to the NCBI36 assembly. DS_2181 ens_36_agfosmid Agincourt Fosmids positioned by pairing SSAHA2 alignments of their sequence ends to the NCBI36 assembly. DS_2182 ens_36_chori17 CHORI 17 BAC DAS Source For 36 Human Assembly: The BAC end read sequences have been mapped to the NCBI36 Human assembly using SSAHA2 and the BACs positioned from suitable alignment pairs. DS_2183 swat_m36_Rassf1aMV Rassf1aMV -- Viral insertion sites SSAHA2 mapped to NCBI M36 assembly (RT35882). DS_2184 swat_m33_Nanog Binding sites for Nanog on NCBI M33 assembly (source doi:10.1038/ng1760). DS_2185 swat_m36_Nanog Binding sites for Nanog mapped (using LiftOver) onto NCBI M36 assembly from M33 (source doi:10.1038/ng1760). DS_2186 swat_m33_Oct4 Binding sites for Oct4 on NCBI M33 assembly (source doi:10.1038/ng1760). DS_2187 swat_m36_Oct4 Binding sites for Oct4 mapped (using LiftOver) onto NCBI M36 assembly from M33 (source doi:10.1038/ng1760). DS_2188 ens_m37_micer ens_m37_micer DS_2189 iPfamDomain Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2190 ens_m33_nodclone NCBI Mouse 33 NOD Clones DS_2191 ens_ncbi_35_32krearray BACPAC 32K Rearray DS_2192 ens_ncbi_35_bacend BAC End Pairs DS_2193 ens_ncbi_35_fosmid Fosmid End Pairs DS_2194 ens_rgsc_31_bacend RAT BAC End Pairs DS_2195 ens_rgsc_31_fgenes Rat fgenes Predictions DS_2196 ens_rgsc_31_gnomon Rat Gnomon Predictions DS_2197 ens_rgsc_31_ncbi NCBI Genes DS_2198 ens_rgsc_31_refseq Rat Refseq DS_2199 ens_rgsc_31_rgdgene RGD genes DS_2200 ens_rgsc_31_twinscan Twinscan Gene Predictions DS_2201 Mouse Fosmids at Sanger A special subset of all mouse fosmids (those with clones available at WT Sanger Institute) mapped to M37 DS_2202 GRC region zebrafish genome Zv9 Region reported to the Genome Reference Consortium Zv9 DS_2203 evigan_predictions Alternative splice site predictions from the program Evigan by Qian Liu. DS_2204 Ailuropoda_melanoleuca.ailMel1.prediction_transcri Annotation source for Ailuropoda_melanoleuca prediction_transcript DS_2205 Ailuropoda_melanoleuca.ailMel1.reference Ailuropoda_melanoleuca Reference server based on ailMel1 assembly. Contains 81466 top level entries. DS_2206 Ailuropoda_melanoleuca.ailMel1.transcript Annotation source for Ailuropoda_melanoleuca transcript DS_2207 Ailuropoda_melanoleuca.ailMel1.translation Annotation source for Ailuropoda_melanoleuca translation DS_2208 Danio_rerio.Zv9.prediction_transcript Annotation source for Danio_rerio prediction_transcript DS_2210 Danio_rerio.Zv9.reference Danio_rerio Reference server based on Zv9 assembly. Contains 1133 top level entries. DS_2212 Danio_rerio.Zv9.transcript Annotation source for Danio_rerio transcript DS_2214 Danio_rerio.Zv9.translation Annotation source for Danio_rerio translation DS_2215 PED The Pancreatic Expression database (PED, http://www.pancreasexpression.org) is the main repository for pancreatic cancer derived -omics data DS_2223 Mus_musculus.VEGA41-clone.transcript Annotation source (returns clones) for Mus_musculus transcript DS_2224 Mus_musculus.VEGA41-clone.translation Annotation source (returns clones) for Mus_musculus translation DS_2225 Mus_musculus.VEGA41.karyotype Annotation source for Mus_musculus karyotype DS_2226 Mus_musculus.VEGA41.prediction_transcript Annotation source for Mus_musculus prediction_transcript DS_2227 Mus_musculus.VEGA41.reference Mus_musculus Reference server based on VEGA41 assembly. Contains 40 top level entries. DS_2228 Mus_musculus.VEGA41.transcript Annotation source for Mus_musculus transcript DS_2229 Mus_musculus.VEGA41.translation Annotation source for Mus_musculus translation DS_2312 Anolis_carolinensis.AnoCar2.0.prediction_transcrip Annotation source for Anolis_carolinensis prediction_transcript DS_2315 Anolis_carolinensis.AnoCar2.0.reference Anolis_carolinensis Reference server based on AnoCar2.0 assembly. Contains 6456 top level entries. DS_2318 Anolis_carolinensis.AnoCar2.0.transcript Annotation source for Anolis_carolinensis transcript DS_2321 Anolis_carolinensis.AnoCar2.0.translation Annotation source for Anolis_carolinensis translation DS_2324 Bos_taurus.Btau_4.0.reference Bos_taurus Reference server based on Btau_4.0 assembly. Contains 12008 top level entries. DS_2326 Bos_taurus.Btau_4.0.transcript Annotation source for Bos_taurus transcript DS_2328 Bos_taurus.Btau_4.0.translation Annotation source for Bos_taurus translation DS_2330 Caenorhabditis_elegans.WS220.reference Caenorhabditis_elegans Reference server based on WS220 assembly. Contains 7 top level entries. DS_2331 Caenorhabditis_elegans.WS220.transcript Annotation source for Caenorhabditis_elegans transcript DS_2332 Caenorhabditis_elegans.WS220.translation Annotation source for Caenorhabditis_elegans translation DS_2333 Callithrix_jacchus.C_jacchus3.2.1.prediction_trans Annotation source for Callithrix_jacchus prediction_transcript DS_2336 Callithrix_jacchus.C_jacchus3.2.1.reference Callithrix_jacchus Reference server based on C_jacchus3.2.1 assembly. Contains 14205 top level entries. DS_2339 Callithrix_jacchus.C_jacchus3.2.1.transcript Annotation source for Callithrix_jacchus transcript DS_2342 Callithrix_jacchus.C_jacchus3.2.1.translation Annotation source for Callithrix_jacchus translation DS_2345 Canis_familiaris.BROADD2.reference Canis_familiaris Reference server based on BROADD2 assembly. Contains 41 top level entries. DS_2346 Canis_familiaris.BROADD2.transcript Annotation source for Canis_familiaris transcript DS_2347 Canis_familiaris.BROADD2.translation Annotation source for Canis_familiaris translation DS_2348 Cavia_porcellus.cavPor3.reference Cavia_porcellus Reference server based on cavPor3 assembly. Contains 3144 top level entries. DS_2349 Cavia_porcellus.cavPor3.transcript Annotation source for Cavia_porcellus transcript DS_2350 Cavia_porcellus.cavPor3.translation Annotation source for Cavia_porcellus translation DS_2351 Choloepus_hoffmanni.choHof1.prediction_transcript Annotation source for Choloepus_hoffmanni prediction_transcript DS_2353 Choloepus_hoffmanni.choHof1.reference Choloepus_hoffmanni Reference server based on choHof1 assembly. Contains 454510 top level entries. DS_2355 Choloepus_hoffmanni.choHof1.transcript Annotation source for Choloepus_hoffmanni transcript DS_2357 Choloepus_hoffmanni.choHof1.translation Annotation source for Choloepus_hoffmanni translation DS_2359 Ciona_intestinalis.JGI2.reference Ciona_intestinalis Reference server based on JGI2 assembly. Contains 4390 top level entries. DS_2361 Ciona_intestinalis.JGI2.transcript Annotation source for Ciona_intestinalis transcript DS_2363 Ciona_intestinalis.JGI2.translation Annotation source for Ciona_intestinalis translation DS_2365 Ciona_savignyi.CSAV2.0.reference Ciona_savignyi Reference server based on CSAV2.0 assembly. Contains 374 top level entries. DS_2366 Ciona_savignyi.CSAV2.0.transcript Annotation source for Ciona_savignyi transcript DS_2367 Ciona_savignyi.CSAV2.0.translation Annotation source for Ciona_savignyi translation DS_2368 Dasypus_novemcinctus.dasNov2.prediction_transcript Annotation source for Dasypus_novemcinctus prediction_transcript DS_2370 Dasypus_novemcinctus.dasNov2.reference Dasypus_novemcinctus Reference server based on dasNov2 assembly. Contains 271554 top level entries. DS_2372 Dasypus_novemcinctus.dasNov2.transcript Annotation source for Dasypus_novemcinctus transcript DS_2374 Dasypus_novemcinctus.dasNov2.translation Annotation source for Dasypus_novemcinctus translation DS_2376 Dipodomys_ordii.dipOrd1.reference Dipodomys_ordii Reference server based on dipOrd1 assembly. Contains 195994 top level entries. DS_2378 Dipodomys_ordii.dipOrd1.transcript Annotation source for Dipodomys_ordii transcript DS_2380 Dipodomys_ordii.dipOrd1.translation Annotation source for Dipodomys_ordii translation DS_2382 Drosophila_melanogaster.BDGP5.25.karyotype Annotation source for Drosophila_melanogaster karyotype DS_2383 Drosophila_melanogaster.BDGP5.25.prediction_transc Annotation source for Drosophila_melanogaster prediction_transcript DS_2384 Drosophila_melanogaster.BDGP5.25.reference Drosophila_melanogaster Reference server based on BDGP5.25 assembly. Contains 15 top level entries. DS_2385 Drosophila_melanogaster.BDGP5.25.transcript Annotation source for Drosophila_melanogaster transcript DS_2386 Drosophila_melanogaster.BDGP5.25.translation Annotation source for Drosophila_melanogaster translation DS_2387 Echinops_telfairi.TENREC.reference Echinops_telfairi Reference server based on TENREC assembly. Contains 297967 top level entries. DS_2389 Echinops_telfairi.TENREC.transcript Annotation source for Echinops_telfairi transcript DS_2391 Echinops_telfairi.TENREC.translation Annotation source for Echinops_telfairi translation DS_2393 Equus_caballus.EquCab2.reference Equus_caballus Reference server based on EquCab2 assembly. Contains 9636 top level entries. DS_2394 Equus_caballus.EquCab2.transcript Annotation source for Equus_caballus transcript DS_2395 Equus_caballus.EquCab2.translation Annotation source for Equus_caballus translation DS_2396 Erinaceus_europaeus.HEDGEHOG.reference Erinaceus_europaeus Reference server based on HEDGEHOG assembly. Contains 352700 top level entries. DS_2398 Erinaceus_europaeus.HEDGEHOG.transcript Annotation source for Erinaceus_europaeus transcript DS_2400 Erinaceus_europaeus.HEDGEHOG.translation Annotation source for Erinaceus_europaeus translation DS_2402 Felis_catus.CAT.reference Felis_catus Reference server based on CAT assembly. Contains 202870 top level entries. DS_2404 Felis_catus.CAT.transcript Annotation source for Felis_catus transcript DS_2406 Felis_catus.CAT.translation Annotation source for Felis_catus translation DS_2408 Gallus_gallus.WASHUC2.reference Gallus_gallus Reference server based on WASHUC2 assembly. Contains 57 top level entries. DS_2409 Gallus_gallus.WASHUC2.transcript Annotation source for Gallus_gallus transcript DS_2410 Gallus_gallus.WASHUC2.translation Annotation source for Gallus_gallus translation DS_2411 Gasterosteus_aculeatus.BROADS1.reference Gasterosteus_aculeatus Reference server based on BROADS1 assembly. Contains 1844 top level entries. DS_2413 Gasterosteus_aculeatus.BROADS1.transcript Annotation source for Gasterosteus_aculeatus transcript DS_2415 Gasterosteus_aculeatus.BROADS1.translation Annotation source for Gasterosteus_aculeatus translation DS_2417 Gorilla_gorilla.gorGor3.prediction_transcript Annotation source for Gorilla_gorilla prediction_transcript DS_2418 Gorilla_gorilla.gorGor3.reference Gorilla_gorilla Reference server based on gorGor3 assembly. Contains 50196 top level entries. DS_2419 Gorilla_gorilla.gorGor3.transcript Annotation source for Gorilla_gorilla transcript DS_2420 Gorilla_gorilla.gorGor3.translation Annotation source for Gorilla_gorilla translation DS_2421 Homo_sapiens.GRCh37.cagetags Annotation source for Homo_sapiens cagetags DS_2423 Homo_sapiens.GRCh37.ditags Annotation source for Homo_sapiens ditags DS_2425 Homo_sapiens.GRCh37.karyotype Annotation source for Homo_sapiens karyotype DS_2427 Homo_sapiens.GRCh37.prediction_transcript Annotation source for Homo_sapiens prediction_transcript DS_2429 Homo_sapiens.GRCh37.reference Homo_sapiens Reference server based on GRCh37 assembly. Contains 177 top level entries. DS_2431 Homo_sapiens.GRCh37.transcript Annotation source for Homo_sapiens transcript DS_2433 Loxodonta_africana.loxAfr3.prediction_transcript Annotation source for Loxodonta_africana prediction_transcript DS_2434 Loxodonta_africana.loxAfr3.reference Loxodonta_africana Reference server based on loxAfr3 assembly. Contains 2352 top level entries. DS_2435 Loxodonta_africana.loxAfr3.transcript Annotation source for Loxodonta_africana transcript DS_2436 Loxodonta_africana.loxAfr3.translation Annotation source for Loxodonta_africana translation DS_2437 Macaca_mulatta.MMUL_1.reference Macaca_mulatta Reference server based on MMUL_1 assembly. Contains 121811 top level entries. DS_2439 Macaca_mulatta.MMUL_1.transcript Annotation source for Macaca_mulatta transcript DS_2441 Macaca_mulatta.MMUL_1.translation Annotation source for Macaca_mulatta translation DS_2443 Macropus_eugenii.Meug_1.0.prediction_transcript Annotation source for Macropus_eugenii prediction_transcript DS_2445 Macropus_eugenii.Meug_1.0.reference Macropus_eugenii Reference server based on Meug_1.0 assembly. Contains 582687 top level entries. DS_2447 Macropus_eugenii.Meug_1.0.transcript Annotation source for Macropus_eugenii transcript DS_2449 Macropus_eugenii.Meug_1.0.translation Annotation source for Macropus_eugenii translation DS_2451 Meleagris_gallopavo.UMD2.prediction_transcript Annotation source for Meleagris_gallopavo prediction_transcript DS_2454 Meleagris_gallopavo.UMD2.reference Meleagris_gallopavo Reference server based on UMD2 assembly. Contains 6165 top level entries. DS_2457 Meleagris_gallopavo.UMD2.transcript Annotation source for Meleagris_gallopavo transcript DS_2460 Meleagris_gallopavo.UMD2.translation Annotation source for Meleagris_gallopavo translation DS_2463 Microcebus_murinus.micMur1.reference Microcebus_murinus Reference server based on micMur1 assembly. Contains 172937 top level entries. DS_2465 Microcebus_murinus.micMur1.transcript Annotation source for Microcebus_murinus transcript DS_2467 Microcebus_murinus.micMur1.translation Annotation source for Microcebus_murinus translation DS_2469 Monodelphis_domestica.BROADO5.reference Monodelphis_domestica Reference server based on BROADO5 assembly. Contains 11 top level entries. DS_2470 Monodelphis_domestica.BROADO5.transcript Annotation source for Monodelphis_domestica transcript DS_2471 Monodelphis_domestica.BROADO5.translation Annotation source for Monodelphis_domestica translation DS_2472 Multi.Ensembl-GeneID.spine Gene Summary Annotation source DS_2473 Mus_musculus.NCBIM37.cagetags Annotation source for Mus_musculus cagetags DS_2475 Mus_musculus.NCBIM37.ditags Annotation source for Mus_musculus ditags DS_2477 Mus_musculus.NCBIM37.karyotype Annotation source for Mus_musculus karyotype DS_2479 Mus_musculus.NCBIM37.prediction_transcript Annotation source for Mus_musculus prediction_transcript DS_2481 Mus_musculus.NCBIM37.reference Mus_musculus Reference server based on NCBIM37 assembly. Contains 211 top level entries. DS_2483 Mus_musculus.NCBIM37.transcript Annotation source for Mus_musculus transcript DS_2485 Mus_musculus.NCBIM37.translation Annotation source for Mus_musculus translation DS_2493 Ochotona_princeps.pika.reference Ochotona_princeps Reference server based on pika assembly. Contains 193095 top level entries. DS_2495 Ochotona_princeps.pika.transcript Annotation source for Ochotona_princeps transcript DS_2497 Ochotona_princeps.pika.translation Annotation source for Ochotona_princeps translation DS_2499 Ornithorhynchus_anatinus.OANA5.reference Ornithorhynchus_anatinus Reference server based on OANA5 assembly. Contains 291092 top level entries. DS_2502 Ornithorhynchus_anatinus.OANA5.transcript Annotation source for Ornithorhynchus_anatinus transcript DS_2505 Ornithorhynchus_anatinus.OANA5.translation Annotation source for Ornithorhynchus_anatinus translation DS_2508 Oryctolagus_cuniculus.oryCun2.prediction_transcrip Annotation source for Oryctolagus_cuniculus prediction_transcript DS_2509 Oryctolagus_cuniculus.oryCun2.reference Oryctolagus_cuniculus Reference server based on oryCun2 assembly. Contains 3241 top level entries. DS_2510 Oryctolagus_cuniculus.oryCun2.transcript Annotation source for Oryctolagus_cuniculus transcript DS_2511 Oryctolagus_cuniculus.oryCun2.translation Annotation source for Oryctolagus_cuniculus translation DS_2512 Oryzias_latipes.MEDAKA1.ditags Annotation source for Oryzias_latipes ditags DS_2515 Oryzias_latipes.MEDAKA1.prediction_transcript Annotation source for Oryzias_latipes prediction_transcript DS_2518 Oryzias_latipes.MEDAKA1.reference Oryzias_latipes Reference server based on MEDAKA1 assembly. Contains 7188 top level entries. DS_2521 Oryzias_latipes.MEDAKA1.transcript Annotation source for Oryzias_latipes transcript DS_2524 Oryzias_latipes.MEDAKA1.translation Annotation source for Oryzias_latipes translation DS_2527 Otolemur_garnettii.BUSHBABY1.reference Otolemur_garnettii Reference server based on BUSHBABY1 assembly. Contains 107969 top level entries. DS_2529 Otolemur_garnettii.BUSHBABY1.transcript Annotation source for Otolemur_garnettii transcript DS_2531 Otolemur_garnettii.BUSHBABY1.translation Annotation source for Otolemur_garnettii translation DS_2533 Pan_troglodytes.CHIMP2.1.reference Pan_troglodytes Reference server based on CHIMP2.1 assembly. Contains 52 top level entries. DS_2534 Pan_troglodytes.CHIMP2.1.transcript Annotation source for Pan_troglodytes transcript DS_2535 Pan_troglodytes.CHIMP2.1.translation Annotation source for Pan_troglodytes translation DS_2539 Procavia_capensis.proCap1.reference Procavia_capensis Reference server based on proCap1 assembly. Contains 277109 top level entries. DS_2541 Procavia_capensis.proCap1.transcript Annotation source for Procavia_capensis transcript DS_2543 Procavia_capensis.proCap1.translation Annotation source for Procavia_capensis translation DS_2545 Pteropus_vampyrus.pteVam1.reference Pteropus_vampyrus Reference server based on pteVam1 assembly. Contains 90637 top level entries. DS_2547 Pteropus_vampyrus.pteVam1.transcript Annotation source for Pteropus_vampyrus transcript DS_2549 Pteropus_vampyrus.pteVam1.translation Annotation source for Pteropus_vampyrus translation DS_2551 Rattus_norvegicus.RGSC3.4.karyotype Annotation source for Rattus_norvegicus karyotype DS_2552 Rattus_norvegicus.RGSC3.4.reference Rattus_norvegicus Reference server based on RGSC3.4 assembly. Contains 22 top level entries. DS_2553 Rattus_norvegicus.RGSC3.4.transcript Annotation source for Rattus_norvegicus transcript DS_2554 Rattus_norvegicus.RGSC3.4.translation Annotation source for Rattus_norvegicus translation DS_2558 Sorex_araneus.COMMON_SHREW1.reference Sorex_araneus Reference server based on COMMON_SHREW1 assembly. Contains 243136 top level entries. DS_2560 Sorex_araneus.COMMON_SHREW1.transcript Annotation source for Sorex_araneus transcript DS_2562 Sorex_araneus.COMMON_SHREW1.translation Annotation source for Sorex_araneus translation DS_2564 Spermophilus_tridecemlineatus.SQUIRREL.reference Spermophilus_tridecemlineatus Reference server based on SQUIRREL assembly. Contains 147878 top level entries. DS_2566 Spermophilus_tridecemlineatus.SQUIRREL.transcript Annotation source for Spermophilus_tridecemlineatus transcript DS_2568 Spermophilus_tridecemlineatus.SQUIRREL.translation Annotation source for Spermophilus_tridecemlineatus translation DS_2570 Sus_scrofa.Sscrofa9.prediction_transcript Annotation source for Sus_scrofa prediction_transcript DS_2571 Sus_scrofa.Sscrofa9.reference Sus_scrofa Reference server based on Sscrofa9 assembly. Contains 20 top level entries. DS_2572 Sus_scrofa.Sscrofa9.transcript Annotation source for Sus_scrofa transcript DS_2573 Sus_scrofa.Sscrofa9.translation Annotation source for Sus_scrofa translation DS_2574 Taeniopygia_guttata.taeGut3.2.4.prediction_transcr Annotation source for Taeniopygia_guttata prediction_transcript DS_2575 Taeniopygia_guttata.taeGut3.2.4.reference Taeniopygia_guttata Reference server based on taeGut3.2.4 assembly. Contains 69 top level entries. DS_2576 Taeniopygia_guttata.taeGut3.2.4.transcript Annotation source for Taeniopygia_guttata transcript DS_2577 Taeniopygia_guttata.taeGut3.2.4.translation Annotation source for Taeniopygia_guttata translation DS_2578 Takifugu_rubripes.FUGU4.reference Takifugu_rubripes Reference server based on FUGU4 assembly. Contains 7214 top level entries. DS_2579 Takifugu_rubripes.FUGU4.transcript Annotation source for Takifugu_rubripes transcript DS_2580 Takifugu_rubripes.FUGU4.translation Annotation source for Takifugu_rubripes translation DS_2581 Tarsius_syrichta.tarSyr1.reference Tarsius_syrichta Reference server based on tarSyr1 assembly. Contains 631266 top level entries. DS_2583 Tarsius_syrichta.tarSyr1.transcript Annotation source for Tarsius_syrichta transcript DS_2585 Tarsius_syrichta.tarSyr1.translation Annotation source for Tarsius_syrichta translation DS_2587 Tetraodon_nigroviridis.TETRAODON8.reference Tetraodon_nigroviridis Reference server based on TETRAODON8 assembly. Contains 27 top level entries. DS_2588 Tetraodon_nigroviridis.TETRAODON8.transcript Annotation source for Tetraodon_nigroviridis transcript DS_2589 Tetraodon_nigroviridis.TETRAODON8.translation Annotation source for Tetraodon_nigroviridis translation DS_2590 Tupaia_belangeri.TREESHREW.reference Tupaia_belangeri Reference server based on TREESHREW assembly. Contains 137753 top level entries. DS_2592 Tupaia_belangeri.TREESHREW.transcript Annotation source for Tupaia_belangeri transcript DS_2594 Tupaia_belangeri.TREESHREW.translation Annotation source for Tupaia_belangeri translation DS_2596 Tursiops_truncatus.turTru1.reference Tursiops_truncatus Reference server based on turTru1 assembly. Contains 111212 top level entries. DS_2598 Tursiops_truncatus.turTru1.transcript Annotation source for Tursiops_truncatus transcript DS_2600 Tursiops_truncatus.turTru1.translation Annotation source for Tursiops_truncatus translation DS_2602 Vicugna_pacos.vicPac1.reference Vicugna_pacos Reference server based on vicPac1 assembly. Contains 290926 top level entries. DS_2604 Vicugna_pacos.vicPac1.transcript Annotation source for Vicugna_pacos transcript DS_2606 Vicugna_pacos.vicPac1.translation Annotation source for Vicugna_pacos translation DS_2611 TEPIDAS TEPIDAS DS_2612 BCCTB Breast Cancer Campaign Tissue Bank Bioinformatics Portal DS_2613 gencode_exp_verification Tested Gencode transcript splice junctions from experimental validation (UNIL) DS_2614 unc_msdas peptides Mass-Spec peptides mapped to GRCh37 6-frame translations (Univ. North Carolina) DS_2615 pjazz_berghei pJazz large-fragment library by O. Billker group DS_2616 EA_regions_36 Affy 500K (redon et al) mapped to NCBI 36 DS_2617 ens_35_aceview Note: the coordinate system for this source was guessed by an automated proceedure at the sanger - if you think this is incorrect please email das-core@sanger.ac.uk with the source id DS_2618 swat_34_rearrangement_hotspots The 130 rearrangement hotspots from doi:10.1038/ng1862 on NCBI34 HG16. DS_2619 swat_36_rearrangement_hotspots 95 of the 130 Rearrangement hotspots from doi:10.1038/ng1862 successfully mapped (from NCBI34 HG16) to NCBI36 HG18 (using UCSC's liftOver). DS_2620 swat_m36_p717tags Mapped insertion tags DS_2621 decipher_archive_ncbi36 DECIPHER V5.0 DS_2627 Selectome Selectome is a database of positive selection on gene trees. DS_2722 Nomascus_leucogenys.Nleu1.0.prediction_transcript Annotation source for Nomascus_leucogenys prediction_transcript DS_2724 Nomascus_leucogenys.Nleu1.0.reference Nomascus_leucogenys Reference server based on Nleu1.0 assembly. Contains 17968 top level entries. DS_2726 Nomascus_leucogenys.Nleu1.0.transcript Annotation source for Nomascus_leucogenys transcript DS_2728 Nomascus_leucogenys.Nleu1.0.translation Annotation source for Nomascus_leucogenys translation DS_2730 Pongo_abelii.PPYG2.prediction_transcript Annotation source for Pongo_abelii prediction_transcript DS_2731 Pongo_abelii.PPYG2.reference Pongo_abelii Reference server based on PPYG2 assembly. Contains 55 top level entries. DS_2732 Pongo_abelii.PPYG2.transcript Annotation source for Pongo_abelii transcript DS_2733 Pongo_abelii.PPYG2.translation Annotation source for Pongo_abelii translation DS_2734 Xenopus_tropicalis.JGI_4.2.prediction_transcript Annotation source for Xenopus_tropicalis prediction_transcript DS_2735 Xenopus_tropicalis.JGI_4.2.reference Xenopus_tropicalis Reference server based on JGI_4.2 assembly. Contains 19549 top level entries. DS_2736 Xenopus_tropicalis.JGI_4.2.transcript Annotation source for Xenopus_tropicalis transcript DS_2737 Xenopus_tropicalis.JGI_4.2.translation Annotation source for Xenopus_tropicalis translation DS_2738 DARNED RNA editing instances in human. DS_2739 testbam test bam registration DS_2740 Danio_rerio.VEGA43-clone.transcript Annotation source (returns clones) for Danio_rerio transcript DS_2741 Danio_rerio.VEGA43-clone.translation Annotation source (returns clones) for Danio_rerio translation DS_2742 Danio_rerio.VEGA43.prediction_transcript Annotation source for Danio_rerio prediction_transcript DS_2743 Danio_rerio.VEGA43.reference Danio_rerio Reference server based on VEGA43 assembly. Contains 27 top level entries. DS_2744 Danio_rerio.VEGA43.transcript Annotation source for Danio_rerio transcript DS_2745 Danio_rerio.VEGA43.translation Annotation source for Danio_rerio translation DS_2746 Homo_sapiens.VEGA43-clone.transcript Annotation source (returns clones) for Homo_sapiens transcript DS_2747 Homo_sapiens.VEGA43-clone.translation Annotation source (returns clones) for Homo_sapiens translation DS_2748 Homo_sapiens.VEGA43.karyotype Annotation source for Homo_sapiens karyotype DS_2749 Homo_sapiens.VEGA43.prediction_transcript Annotation source for Homo_sapiens prediction_transcript DS_2750 Homo_sapiens.VEGA43.reference Homo_sapiens Reference server based on VEGA43 assembly. Contains 39 top level entries. DS_2751 Homo_sapiens.VEGA43.transcript Annotation source for Homo_sapiens transcript DS_2752 Homo_sapiens.VEGA43.translation Annotation source for Homo_sapiens translation DS_2753 Cafe Variome Diagnostic Variants (human GRCh 37) Cafe Variome - diagnostic variants (Human GRCh 37) DS_2754 ctcf_ptr blady blah DS_2755 Sample BAM file from Loraine Lab 75 base single end Illumina reads aligned onto the A_thaliana_Jun_2009 (TAIR9) genome assembly using TopHat. The library was prepared from three week old seedlings undergoing simulated drought stress. DS_2756 Myotis_lucifugus.Myoluc2.0.prediction_transcript Annotation source for Myotis_lucifugus prediction_transcript DS_2757 Myotis_lucifugus.Myoluc2.0.reference Myotis_lucifugus Reference server based on Myoluc2.0 assembly. Contains 11654 top level entries. DS_2758 Myotis_lucifugus.Myoluc2.0.transcript Annotation source for Myotis_lucifugus transcript DS_2759 Myotis_lucifugus.Myoluc2.0.translation Annotation source for Myotis_lucifugus translation DS_2760 Saccharomyces_cerevisiae.EF3.reference Saccharomyces_cerevisiae Reference server based on EF3 assembly. Contains 18 top level entries. DS_2761 Saccharomyces_cerevisiae.EF3.transcript Annotation source for Saccharomyces_cerevisiae transcript DS_2762 Saccharomyces_cerevisiae.EF3.translation Annotation source for Saccharomyces_cerevisiae translation DS_2763 CATH Domains Manually curated structural domain boundaries for PDB structures DS_2764 CATH Domain Homologues in Ensembl. CATH Superfamily domain homologues, identified by sequence similarity, and mapped to Ensembl. DS_2765 CATH Domains in UniProt CATH Structural domains directly mapped to UniProt. A clone of the cath_uniprot server for backwards compatibility. DS_2766 CATH Structural Domain Alignments 3D Alignments of highly structurally similar protein domains DS_2767 CATH Domains in UniProt CATH Structural domains directly mapped to UniProt. DS_2768 CATH Domain Homologues in UniProt. CATH Superfamily domain homologues, identified using DomainFinder.

Go to the output files for this example

Command line arguments

Generates server cache file for DAS servers or for the DAS registry
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-cachefile]         outfile    [server.$(servername)] Server cache output
                                  file

   Additional (Optional) qualifiers:
   -sequencesourcesonly boolean    [N] Display DAS sequence sources only
   -outfile            outfile    [stdout] Output file name

   Advanced (Unprompted) qualifiers:
   -host               string     [www.dasregistry.org] DAS registry/server
                                  host location (Any string)
   -path               string     [/das] DAS registry/server path on
                                  registry/server host (Any string)
   -port               integer    [80] DAS registry/server port on
                                  registry/server host (Any integer value)
   -servername         string     [das] Name of a DAS server defined in EMBOSS
                                  resource files (Any string)

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   "-cachefile" associated qualifiers
   -odirectory1        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-cachefile] (Parameter 1)	outfile	Server cache output file	Output file	server.$(servername)
Additional (Optional) qualifiers
-sequencesourcesonly	boolean	Display DAS sequence sources only	Boolean value Yes/No	No
-outfile	outfile	Output file name	Output file	stdout
Advanced (Unprompted) qualifiers
-host	string	DAS registry/server host location	Any string	www.dasregistry.org
-path	string	DAS registry/server path on registry/server host	Any string	/das
-port	integer	DAS registry/server port on registry/server host	Any integer value	80
-servername	string	Name of a DAS server defined in EMBOSS resource files	Any string	das
Associated qualifiers
"-outfile" associated outfile qualifiers
-odirectory	string	Output directory	Any string
"-cachefile" associated outfile qualifiers
-odirectory1 -odirectory_cachefile	string	Output directory	Any string
General qualifiers
-auto	boolean	Turn off prompts	Boolean value Yes/No	N
-stdout	boolean	Write first file to standard output	Boolean value Yes/No	N
-filter	boolean	Read first file from standard input, write first file to standard output	Boolean value Yes/No	N
-options	boolean	Prompt for standard and additional values	Boolean value Yes/No	N
-debug	boolean	Write debug output to program.dbg	Boolean value Yes/No	N
-verbose	boolean	Report some/full command line options	Boolean value Yes/No	Y
-help	boolean	Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose	Boolean value Yes/No	N
-warning	boolean	Report warnings	Boolean value Yes/No	Y
-error	boolean	Report errors	Boolean value Yes/No	Y
-fatal	boolean	Report fatal errors	Boolean value Yes/No	Y
-die	boolean	Report dying program messages	Boolean value Yes/No	Y
-version	boolean	Report version number and exit	Boolean value Yes/No	N

Input file format

Output file format

Output files for usage example

File: qatests.server.dasregistry

# qatests.server.dasregistry 2011-07-15 12:00:00

DB cath [
  method: das
  type: "Protfeatures"
  format: "dasgff"
  url: http://cathdb.info:9000/das/cath_pdb
  example: "5pti"
  comment: "The CATH database annotates PDB structures with CATH structural domains as derived from a combination of automatic and manually methods."
  hasaccession: "N"
  identifier: "segment"
  fields: "segment,type,category,categorize,feature_id"
]

DB DS_114_signalp [
  method: das
  type: "Protfeatures"
  format: "dasgff"
  url: http://das.cbs.dtu.dk:9000/das/signalp
  example: "ALBU_HUMAN"
  comment: "SignalP (http://www.cbs.dtu.dk/services/SignalP) predictions for UniProt."
  hasaccession: "N"
  identifier: "segment"
  fields: "segment,type,category,categorize,feature_id"
]

DB netphos [
  method: das
  type: "Protfeatures"
  format: "dasgff"
  url: http://das.cbs.dtu.dk:9000/das/netphos
  example: "ALBU_HUMAN"
  comment: "NetPhos (http://www.cbs.dtu.dk/services/NetPhos) predictions for UniProt."
  hasaccession: "N"
  identifier: "segment"
  fields: "segment,type,category,categorize,feature_id"
]

DB prop [
  method: das
  type: "Protfeatures"
  format: "dasgff"
  url: http://das.cbs.dtu.dk:9000/das/prop
  example: "GDNF_HUMAN"
  comment: "ProP (http://www.cbs.dtu.dk/services/ProP) predictions for UniProt."
  hasaccession: "N"
  identifier: "segment"
  fields: "segment,type,category,categorize,feature_id"
]



  [Part of this file has been deleted for brevity]

  fields: "segment,type,category,categorize,feature_id"
]

DB CATH_Domain_Homologues_in_Ensembl [
  method: das
  type: "Protfeatures"
  format: "dasgff"
  url: http://das.cathdb.info/das/gene3d_ensembl
  example: "ENSGACP00000019937"
  comment: "CATH Superfamily domain homologues, identified by sequence similarity, and mapped to Ensembl."
  hasaccession: "N"
  identifier: "segment"
  fields: "segment,type,category,categorize,feature_id"
]

DB DS_2765_CATH_Domains_in_UniProt [
  method: das
  type: "Protfeatures"
  format: "dasgff"
  url: http://das.cathdb.info/das/cath_sptr
  example: "P20279"
  comment: "CATH Structural domains directly mapped to UniProt. A clone of the cath_uniprot server for backwards compatibility."
  hasaccession: "N"
  identifier: "segment"
  fields: "segment,type,category,categorize,feature_id"
]

DB DS_2767_CATH_Domains_in_UniProt [
  method: das
  type: "Protfeatures"
  format: "dasgff"
  url: http://das.cathdb.info/das/cath_uniprot
  example: "P20279"
  comment: "CATH Structural domains directly mapped to UniProt."
  hasaccession: "N"
  identifier: "segment"
  fields: "segment,type,category,categorize,feature_id"
]

DB CATH_Domain_Homologues_in_UniProt [
  method: das
  type: "Protfeatures"
  format: "dasgff"
  url: http://das.cathdb.info/das/gene3d_cath
  example: "P15498"
  comment: "CATH Superfamily domain homologues, identified using DomainFinder."
  hasaccession: "N"
  identifier: "segment"
  fields: "segment,type,category,categorize,feature_id"
]

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Target users

Comments