esim4 |
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The program is available for download from http://globin.cse.psu.edu/
% esim4 Align an mRNA to a genomic DNA sequence Input nucleotide sequence: tembl:h45989 Genomic sequence: tembl:z69719 Sim4 program output file [h45989.esim4]: |
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Align an mRNA to a genomic DNA sequence Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-asequence] sequence Nucleotide sequence filename and optional format, or reference (input USA) [-bsequence] seqall Genomic sequence [-outfile] outfile [*.esim4] Sim4 program output file Additional (Optional) qualifiers (* if not always prompted): -word integer [12] Sets the word size (W) for blast hits (Any integer value) -extend integer [12] Sets the word extension termination limit (X) for the blast-like stage of the algorithm. (Any integer value) -cutoff integer [3] Sets the cutoff (E) in range [3,10]. (Integer up to 10) -useramsp toggle [N] False: esim4 calculates mspA, True: value from mspA command line argument. * -amsp integer [16] MSP score threshold (K) for the first stage of the algorithm. (If this option is not specified, the threshold is computed from the lengths of the sequences, using statistical criteria.) For example, a good value for genomic sequences in the range of a few hundred Kb is 16. To avoid spurious matches, however, a larger value may be needed for longer sequences. (Any integer value) -userbmsp toggle [N] False: esim4 calculates mspB, True: value from mspB command line argument. * -bmsp integer [12] Sets the threshold for the MSP scores (C) when aligning the as-yet-unmatched fragments, during the second stage of the algorithm. By default, the smaller of the constant 12 and a statistics-based threshold is chosen. (Any integer value) -weight integer [0] Weight value (H) (undocumented). 0 uses a default, >0 is a value (Any integer value) -diagonal integer [10] Bound (K) for the diagonal distance within consecutive MSPs in an exon. (Any integer value) -strand menu [both] This determines the strand of the genome (R) with which the mRNA will be aligned. The default value is 'both', in which case both strands of the genome are attempted. The other allowed modes are 'forward' and 'reverse'. (Values: both (Both strands); forward (Forward strand only); reverse (Reverse strand only)) -format integer [0] Sets the output format (A). Exon endpoints only (format=0), exon endpoints and boundaries of the coding region (CDS) in the genomic sequence, when specified for the input mRNA (-format=5), alignment text (-format=1), alignment in lav-block format (-format=2), or both exon endpoints and alignment text (-format=3 or -format=4). If a reverse complement match is found, -format=0,1,2,3,5 will give its position in the plus strand of the longer sequence and the minus strand of the shorter sequence. -format=4 will give its position in the plus strand of the first sequence (mRNA) and the minus strand of the second sequence (genome), regardless of which sequence is longer. The -format=5 option can be used with the S command line option to specify the endpoints of the CDS in the mRNA, and produces output in the exons file format required by PipMaker. (Integer from 0 to 5) -cliptails boolean [N] Trim poly-A tails (P). Specifies whether or not the program should report the fragment of the alignment containing the poly-A tail (if found). By default (-nocliptails) the alignment is displayed as computed. When this feature is enabled (-cliptails), sim4 will remove the poly-A tails and all format options will produce additional lav alignment headers. -smallexons boolean [N] Requests an additional search for small marginal exons (N) (N=1) guided by the splice-site recognition signals. This option can be used when a high accuracy match is expected. The default value is N=0, specifying no additional search. -[no]ambiguity boolean [Y] Controls the set of characters allowed in the input sequences (B). By default (-ambiguity), ambiguity characters (ABCDGHKMNRSTVWXY) are allowed. By specifying -noambiguity, the set of acceptable characters is restricted to A,C,G,T,N and X only. -cdsregion string Allows the user to specify the endpoints of the CDS in the input mRNA (S), with the syntax: -cdsregion=n1..n2. This option is only available with the -format=5 flag, which produces output in the format required by PipMaker. Alternatively, the CDS coordinates could appear in a construct CDS=n1..n2 in the FastA header of the mRNA sequence. When the second file is an mRNA database, the command line specification for the CDS will apply to the first sequence in the file only. (Any string) -aoffset integer [0] Undocumented (f) - some sort of offset in first sequence. (Any integer value) -boffset integer [0] Undocumented (F) - some sort of offset in second sequence. (Any integer value) -toa integer [0] Undocumented (t)- offset end of first sequence? (Any integer value) -tob integer [0] Undocumented (T) - offset end of second sequence? (Any integer value) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-asequence" associated qualifiers -sbegin1 integer Start of the sequence to be used -send1 integer End of the sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-bsequence" associated qualifiers -sbegin2 integer Start of each sequence to be used -send2 integer End of each sequence to be used -sreverse2 boolean Reverse (if DNA) -sask2 boolean Ask for begin/end/reverse -snucleotide2 boolean Sequence is nucleotide -sprotein2 boolean Sequence is protein -slower2 boolean Make lower case -supper2 boolean Make upper case -sformat2 string Input sequence format -sdbname2 string Database name -sid2 string Entryname -ufo2 string UFO features -fformat2 string Features format -fopenfile2 string Features file name "-outfile" associated qualifiers -odirectory3 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 | ||||||||||
[-asequence] (Parameter 1) |
sequence | Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required | ||||||
[-bsequence] (Parameter 2) |
seqall | Genomic sequence | Readable sequence(s) | Required | ||||||
[-outfile] (Parameter 3) |
outfile | Sim4 program output file | Output file | <*>.esim4 | ||||||
Additional (Optional) qualifiers | ||||||||||
-word | integer | Sets the word size (W) for blast hits | Any integer value | 12 | ||||||
-extend | integer | Sets the word extension termination limit (X) for the blast-like stage of the algorithm. | Any integer value | 12 | ||||||
-cutoff | integer | Sets the cutoff (E) in range [3,10]. | Integer up to 10 | 3 | ||||||
-useramsp | toggle | False: esim4 calculates mspA, True: value from mspA command line argument. | Toggle value Yes/No | No | ||||||
-amsp | integer | MSP score threshold (K) for the first stage of the algorithm. (If this option is not specified, the threshold is computed from the lengths of the sequences, using statistical criteria.) For example, a good value for genomic sequences in the range of a few hundred Kb is 16. To avoid spurious matches, however, a larger value may be needed for longer sequences. | Any integer value | 16 | ||||||
-userbmsp | toggle | False: esim4 calculates mspB, True: value from mspB command line argument. | Toggle value Yes/No | No | ||||||
-bmsp | integer | Sets the threshold for the MSP scores (C) when aligning the as-yet-unmatched fragments, during the second stage of the algorithm. By default, the smaller of the constant 12 and a statistics-based threshold is chosen. | Any integer value | 12 | ||||||
-weight | integer | Weight value (H) (undocumented). 0 uses a default, >0 is a value | Any integer value | 0 | ||||||
-diagonal | integer | Bound (K) for the diagonal distance within consecutive MSPs in an exon. | Any integer value | 10 | ||||||
-strand | list | This determines the strand of the genome (R) with which the mRNA will be aligned. The default value is 'both', in which case both strands of the genome are attempted. The other allowed modes are 'forward' and 'reverse'. |
|
both | ||||||
-format | integer | Sets the output format (A). Exon endpoints only (format=0), exon endpoints and boundaries of the coding region (CDS) in the genomic sequence, when specified for the input mRNA (-format=5), alignment text (-format=1), alignment in lav-block format (-format=2), or both exon endpoints and alignment text (-format=3 or -format=4). If a reverse complement match is found, -format=0,1,2,3,5 will give its position in the plus strand of the longer sequence and the minus strand of the shorter sequence. -format=4 will give its position in the plus strand of the first sequence (mRNA) and the minus strand of the second sequence (genome), regardless of which sequence is longer. The -format=5 option can be used with the S command line option to specify the endpoints of the CDS in the mRNA, and produces output in the exons file format required by PipMaker. | Integer from 0 to 5 | 0 | ||||||
-cliptails | boolean | Trim poly-A tails (P). Specifies whether or not the program should report the fragment of the alignment containing the poly-A tail (if found). By default (-nocliptails) the alignment is displayed as computed. When this feature is enabled (-cliptails), sim4 will remove the poly-A tails and all format options will produce additional lav alignment headers. | Boolean value Yes/No | No | ||||||
-smallexons | boolean | Requests an additional search for small marginal exons (N) (N=1) guided by the splice-site recognition signals. This option can be used when a high accuracy match is expected. The default value is N=0, specifying no additional search. | Boolean value Yes/No | No | ||||||
-[no]ambiguity | boolean | Controls the set of characters allowed in the input sequences (B). By default (-ambiguity), ambiguity characters (ABCDGHKMNRSTVWXY) are allowed. By specifying -noambiguity, the set of acceptable characters is restricted to A,C,G,T,N and X only. | Boolean value Yes/No | Yes | ||||||
-cdsregion | string | Allows the user to specify the endpoints of the CDS in the input mRNA (S), with the syntax: -cdsregion=n1..n2. This option is only available with the -format=5 flag, which produces output in the format required by PipMaker. Alternatively, the CDS coordinates could appear in a construct CDS=n1..n2 in the FastA header of the mRNA sequence. When the second file is an mRNA database, the command line specification for the CDS will apply to the first sequence in the file only. | Any string | |||||||
-aoffset | integer | Undocumented (f) - some sort of offset in first sequence. | Any integer value | 0 | ||||||
-boffset | integer | Undocumented (F) - some sort of offset in second sequence. | Any integer value | 0 | ||||||
-toa | integer | Undocumented (t)- offset end of first sequence? | Any integer value | 0 | ||||||
-tob | integer | Undocumented (T) - offset end of second sequence? | Any integer value | 0 | ||||||
Advanced (Unprompted) qualifiers | ||||||||||
(none) | ||||||||||
Associated qualifiers | ||||||||||
"-asequence" associated sequence qualifiers | ||||||||||
-sbegin1 -sbegin_asequence |
integer | Start of the sequence to be used | Any integer value | 0 | ||||||
-send1 -send_asequence |
integer | End of the sequence to be used | Any integer value | 0 | ||||||
-sreverse1 -sreverse_asequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N | ||||||
-sask1 -sask_asequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | ||||||
-snucleotide1 -snucleotide_asequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N | ||||||
-sprotein1 -sprotein_asequence |
boolean | Sequence is protein | Boolean value Yes/No | N | ||||||
-slower1 -slower_asequence |
boolean | Make lower case | Boolean value Yes/No | N | ||||||
-supper1 -supper_asequence |
boolean | Make upper case | Boolean value Yes/No | N | ||||||
-sformat1 -sformat_asequence |
string | Input sequence format | Any string | |||||||
-sdbname1 -sdbname_asequence |
string | Database name | Any string | |||||||
-sid1 -sid_asequence |
string | Entryname | Any string | |||||||
-ufo1 -ufo_asequence |
string | UFO features | Any string | |||||||
-fformat1 -fformat_asequence |
string | Features format | Any string | |||||||
-fopenfile1 -fopenfile_asequence |
string | Features file name | Any string | |||||||
"-bsequence" associated seqall qualifiers | ||||||||||
-sbegin2 -sbegin_bsequence |
integer | Start of each sequence to be used | Any integer value | 0 | ||||||
-send2 -send_bsequence |
integer | End of each sequence to be used | Any integer value | 0 | ||||||
-sreverse2 -sreverse_bsequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N | ||||||
-sask2 -sask_bsequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | ||||||
-snucleotide2 -snucleotide_bsequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N | ||||||
-sprotein2 -sprotein_bsequence |
boolean | Sequence is protein | Boolean value Yes/No | N | ||||||
-slower2 -slower_bsequence |
boolean | Make lower case | Boolean value Yes/No | N | ||||||
-supper2 -supper_bsequence |
boolean | Make upper case | Boolean value Yes/No | N | ||||||
-sformat2 -sformat_bsequence |
string | Input sequence format | Any string | |||||||
-sdbname2 -sdbname_bsequence |
string | Database name | Any string | |||||||
-sid2 -sid_bsequence |
string | Entryname | Any string | |||||||
-ufo2 -ufo_bsequence |
string | UFO features | Any string | |||||||
-fformat2 -fformat_bsequence |
string | Features format | Any string | |||||||
-fopenfile2 -fopenfile_bsequence |
string | Features file name | Any string | |||||||
"-outfile" associated outfile qualifiers | ||||||||||
-odirectory3 -odirectory_outfile |
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 |
ID H45989; SV 1; linear; mRNA; EST; HUM; 495 BP. XX AC H45989; XX DT 18-NOV-1995 (Rel. 45, Created) DT 04-MAR-2000 (Rel. 63, Last updated, Version 2) XX DE yo13c02.s1 Soares adult brain N2b5HB55Y Homo sapiens cDNA clone DE IMAGE:177794 3', mRNA sequence. XX KW EST. XX OS Homo sapiens (human) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; OC Homo. XX RN [1] RP 1-495 RA Hillier L., Clark N., Dubuque T., Elliston K., Hawkins M., Holman M., RA Hultman M., Kucaba T., Le M., Lennon G., Marra M., Parsons J., Rifkin L., RA Rohlfing T., Soares M., Tan F., Trevaskis E., Waterston R., Williamson A., RA Wohldmann P., Wilson R.; RT "The WashU-Merck EST Project"; RL Unpublished. XX DR GDB; 3839990. DR GDB; 4193257. DR ImaGenes; ENSEp780A0214D. DR ImaGenes; ENSEp780A044Q. DR ImaGenes; HU3_p972A0639D. DR ImaGenes; HU3_p972B1110Q. DR ImaGenes; HU3_p983A0639D. DR ImaGenes; HU4_p940A0622D. DR ImaGenes; IMAGp956A0431Q. DR ImaGenes; IMAGp998F03326Q. DR ImaGenes; RZPDp1096A101D. DR ImaGenes; RZPDp1096A191Q. DR ImaGenes; RZPDp200A0214D. DR UNILIB; 555; 300. XX CC On May 8, 1995 this sequence version replaced gi:800819. CC Contact: Wilson RK CC Washington University School of Medicine CC 4444 Forest Park Parkway, Box 8501, St. Louis, MO 63108 CC Tel: 314 286 1800 CC Fax: 314 286 1810 CC Email: est@watson.wustl.edu CC Insert Size: 544 CC High quality sequence stops: 265 CC Source: IMAGE Consortium, LLNL CC This clone is available royalty-free through LLNL ; contact the CC IMAGE Consortium (info@image.llnl.gov) for further information. CC Possible reversed clone: polyT not found CC Insert Length: 544 Std Error: 0.00 CC Seq primer: SP6 CC High quality sequence stop: 265. XX FH Key Location/Qualifiers FH FT source 1..495 FT /organism="Homo sapiens" FT /lab_host="DH10B (ampicillin resistant)" FT /mol_type="mRNA" FT /sex="Male" FT /dev_stage="55-year old" FT /clone_lib="Soares adult brain N2b5HB55Y" FT /clone="IMAGE:177794" FT /note="Organ: brain; Vector: pT7T3D (Pharmacia) with a FT modified polylinker; Site_1: Not I; Site_2: Eco RI; 1st FT strand cDNA was primed with a Not I - oligo(dT) primer [5' FT TGTTACCAATCTGAAGTGGGAGCGGCCGCGCTTTTTTTTTTTTTTTTTTT 3'], FT double-stranded cDNA was size selected, ligated to Eco RI FT adapters (Pharmacia), digested with Not I and cloned into FT the Not I and Eco RI sites of a modified pT7T3 vector FT (Pharmacia). Library went through one round of FT normalization to a Cot = 53. Library constructed by Bento FT Soares and M.Fatima Bonaldo. The adult brain RNA was FT provided by Dr. Donald H. Gilden. Tissue was acquired 17-18 FT hours after death which occurred in consequence of a FT ruptured aortic aneurysm. RNA was prepared from a pool of FT tissues representing the following areas of the brain: FT frontal, parietal, temporal and occipital cortex from the FT left and right hemispheres, subcortical white matter, basal FT ganglia, thalamus, cerebellum, midbrain, pons and medulla." FT /db_xref="taxon:9606" FT /db_xref="UNILIB:555" XX SQ Sequence 495 BP; 73 A; 135 C; 169 G; 104 T; 14 other; ccggnaagct cancttggac caccgactct cgantgnntc gccgcgggag ccggntggan 60 aacctgagcg ggactggnag aaggagcaga gggaggcagc acccggcgtg acggnagtgt 120 gtggggcact caggccttcc gcagtgtcat ctgccacacg gaaggcacgg ccacgggcag 180 gggggtctat gatcttctgc atgcccagct ggcatggccc cacgtagagt ggnntggcgt 240 ctcggtgctg gtcagcgaca cgttgtcctg gctgggcagg tccagctccc ggaggacctg 300 gggcttcagc ttcccgtagc gctggctgca gtgacggatg ctcttgcgct gccatttctg 360 ggtgctgtca ctgtccttgc tcactccaaa ccagttcggc ggtccccctg cggatggtct 420 gtgttgatgg acgtttgggc tttgcagcac cggccgccga gttcatggtn gggtnaagag 480 atttgggttt tttcn 495 // |
ID Z69719; SV 1; linear; genomic DNA; STD; HUM; 33760 BP. XX AC Z69719; XX DT 26-FEB-1996 (Rel. 46, Created) DT 13-JAN-2009 (Rel. 99, Last updated, Version 7) XX DE Human DNA sequence from clone XX-CNFG9 on chromosome 16 XX KW C16orf33; HTG; POLR3K; RHBDF1. XX OS Homo sapiens (human) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; OC Homo. XX RN [1] RP 1-33760 RA Kershaw J.; RT ; RL Submitted (09-JAN-2009) to the EMBL/GenBank/DDBJ databases. RL Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK. RL E-mail enquiries: vega@sanger.ac.uk Clone requests: Geneservice RL (http://www.geneservice.co.uk/) and BACPAC Resources RL (http://bacpac.chori.org/) XX DR EMBL-CON; GL000124. DR GDB; 11502921. DR RFAM; RF00017; SRP_euk_arch. XX CC -------------- Genome Center CC Center: Wellcome Trust Sanger Institute CC Center code: SC CC Web site: http://www.sanger.ac.uk CC Contact: vega@sanger.ac.uk CC -------------- CC CC This sequence was finished as follows unless otherwise noted: all regions CC were either double-stranded or sequenced with an alternate chemistry or CC covered by high quality data (i.e., phred quality >= 30); an attempt was CC made to resolve all sequencing problems, such as compressions and repeats; CC all regions were covered by at least one subclone; and the assembly was CC confirmed by restriction digest, except on the rare occasion of the clone CC being a YAC. CC CC The following abbreviations are used to associate primary accession CC numbers given in the feature table with their source databases: CC Em:, EMBL; Sw:, SWISSPROT; Tr:, TREMBL; Wp:, WORMPEP; CC Information on the WORMPEP database can be found at CC http://www.sanger.ac.uk/Projects/C_elegans/wormpep [Part of this file has been deleted for brevity] gagacagcag agtgctcagc tcatgaagga ggcaccagcc gccatgcctc tacatccagg 30840 tctcctgggg ttcccacctc cacaaaaacc cccactgcta ggagtgcagg caggagggga 30900 cctgagaacc gacagttata ggtcctgcgg gtgggcagtg ctgggtgttc tggtctgccc 30960 cacccctgtg tgcctagatc cccatctggg cctcaagtgg gtgggattcc aaaggaagag 31020 ccggagtagg cgtggggagg ggcaggccca ggctggacaa agagtctggc cagggagcgg 31080 cacattgccc tcccagagac agtggctcag tgtccaggcc ttccccaggc gcacagtggg 31140 ctcttgttcc cagaaagccc ctcgggggga tccaaacagt gtctccccca ccccgctgac 31200 ccctcagtgt atggggaaac cgtggcccac ggaaggcctc actgcctggg gtcacacagc 31260 atctgagtca ctgcagcagc ctcacagctg ccagcccagg cccagcccca tcaggagaca 31320 cccaaagcca cagtgcatcc caggaccagc tgggggggct gcgggcagga ctctcgatga 31380 ggctgaggga cgaggagggt caagggagcc actggcgcca tgcatgctga cgtcccctct 31440 ggctgcctgc agagcctggt gtggaagggc tgagtggggg atggtggaga gtcctgttaa 31500 ctcaggtttc tgctctgggg atgtctgggc acccatcaag ctggccgcgt gcacaggtgc 31560 agggagagcc agaaagcagg agccgatgca gggaggccac tggggacagc ccaggctgat 31620 gcttgggccc catgtgtctc caccacctac aaccctaagc aagcctcagc tttcccatct 31680 ggaaatcagg ggtcacagca gtgcctggca cagtagcagc ggctgactcc atcacagggt 31740 ggtgtagcct gtgggtactt ggcactctct gaggggcagg agctgggggg tgaaaggacc 31800 ctagagcata tgcaacaaga gggcagccct ggggacacct ggggacagaa ccctccaaag 31860 gtgtcgagtt tgggaagaga ctagagagaa gctctggcca gtccaggcat agacagtggc 31920 cacagccagt ggagagctgc atcctcaggt gtgagcagca accacctctg tactcaggcc 31980 tgccctgcac actcacagga ccatgctggc agggacaact ggcggcggag ttgactgcca 32040 accccggggc cagaaccatc aagcctgggc tctgctccgc ccaaggaact gcctgctgcc 32100 gaggtcagct ggagcaaggg gcctcacccc gggacacctt cccagacgtg tcctcagctc 32160 acatgagcct catcccaggg ggatgtggct cctccagcat ccccacccac acgctgctct 32220 ctgaccctca gtcttctgtt tgactcctaa tctgaagctc aatcctagat ctcccttgag 32280 aagggggtca ccagctgtct ggcagcccag cctccaggtc ttctggatta atgaagggaa 32340 agtcacctgg cctctctgcc ttgtctatta atggcatcat gctgagaatg atatttgcta 32400 ggccctttgc aaaccccaaa gtgctcttca accctcccag tgaagcctct tcttttctgt 32460 ggaagaaatg aggttcaggg tggagcaggg caggcctgag acctttgcag ggttctctcc 32520 aggtccccag caggacagac tggcaccctg cctcccctca tcaccctaga caaggagaca 32580 gaacaagagg ttccctgcta caggccatct gtgagggaag ccgccctagg gcctgtagac 32640 acaggaatcc ctgaggacct gacctgtgag ggtagtgcac aaaggggcca gcacttggca 32700 ggaggggggg gggcactgcc ccaaggctca gctagcaaat gtggcacagg ggtcaccaga 32760 gctaaacccc tgactcagtt gggtctgaca ggggctgaca tggcagacac acccaggaat 32820 caggggacac caagtgcagc tcagggcacc tgtccaggcc acacagtcag aaaggggatg 32880 gcagcaagga cttagctaca ctagattctg ggggtaaact gcctggtatg ctggtcactg 32940 ctagtcccca gtctggagtc tagctgggtc tcaggagtta ggcgaaaaca ccctccccag 33000 gctgcaggtg ggagaggccc acatcccctg cacacgtctg gccagaggac agatgggcag 33060 cccagtcacc agtcagagcc ctccagaggt gtccctgact gaccctacac acatgcaccc 33120 aggtgcccag gcacccttgg gctcagcaac cctgcaaccc cctcccagga cccaccagaa 33180 gcaggatagg actagagagg ccacaggagg gaaaccaagt cagagcagaa atggcttcgg 33240 tcctcagcag cctggctcag cttcctcaaa ccagatcctg actgatcaca ctggtctgtc 33300 taacccctgg gaggggtcct ctgtatccat cttacagata aggaaactga ggctcagaga 33360 agcccatcac tgcctaaggt cccagggcct ataagggagc tcaaagcctt gggccaggtc 33420 tgcccaggag ctgcagtgga agggaccctg tctgcagacc cccagaagac aaggcagacc 33480 acctgggttc ttcagccttg tggctgtgga cggctgtcag acccttctaa gaccccttgc 33540 cacctgctcc atcaggggca tctcagttga agaaggaagg actcaccccc aaaatcgtcc 33600 aactcagaaa aaaaggcaga agccaaggaa tccaatcact gggcaaaatg tgatcctggc 33660 acagacactg aggtggggga actggagccg gtgtggcgga ggccctcaca gccaagagca 33720 actgggggtg ccctgggcag ggactgtagc tgggaagatc 33760 // |
seq1 = H45989, 495 bp seq2 = Z69719 (Z69719), 33760 bp 1-193 (25686-25874) 92% <- 194-407 (26279-26492) 98% <- 408-487 (27391-27469) 88% |
Program name | Description |
---|---|
est2genome | Align EST sequences to genomic DNA sequence |
needle | Needleman-Wunsch global alignment of two sequences |
needleall | Many-to-many pairwise alignments of two sequence sets |
stretcher | Needleman-Wunsch rapid global alignment of two sequences |
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