SCOPPARSE documentation |
# dir.cla.scop.txt # SCOP release 1.57 (January 2002) [File format version 1.00] # http://scop.mrc-lmb.cam.ac.uk/scop/ # Copyright (c) 1994-2002 the scop authors; see http://scop.mrc-lmb.cam.ac.uk/scop/lic/copy.html d1cs4a_ 1cs4 A: d.58.29.1 39418 cl=53931,cf=54861,sf=55073,fa=55074,dm=55077,sp=55078,px=39418 d1ii7a_ 1ii7 A: d.159.1.4 62415 cl=53931,cf=56299,sf=56300,fa=64427,dm=64428,sp=64429,px=62415 |
# dir.des.scop.txt # SCOP release 1.57 (January 2002) [File format version 1.00] # http://scop.mrc-lmb.cam.ac.uk/scop/ # Copyright (c) 1994-2002 the scop authors; see http://scop.mrc-lmb.cam.ac.uk/scop/lic/copy.html 53931 cl d - Alpha and beta proteins (a+b) 54861 cf d.58 - Ferredoxin-like 55073 sf d.58.29 - Adenylyl and guanylyl cyclase catalytic domain 55074 fa d.58.29.1 - Adenylyl and guanylyl cyclase catalytic domain 55077 dm d.58.29.1 - Adenylyl cyclase VC1, domain C1a 55078 sp d.58.29.1 - Dog (Canis familiaris) 39418 px d.58.29.1 d1cs4a_ 1cs4 A: 56299 cf d.159 - Metallo-dependent phosphatases 56300 sf d.159.1 - Metallo-dependent phosphatases 64427 fa d.159.1.4 - DNA double-strand break repair nuclease 64428 dm d.159.1.4 - Mre11 64429 sp d.159.1.4 - Archaeon Pyrococcus furiosus 62415 px d.159.1.4 d1ii7a_ 1ii7 A: |
ID D1CS4A_ XX EN 1CS4 XX TY SCOP XX SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Adenylyl and guanylyl cyclase catalytic domain XX FA Adenylyl and guanylyl cyclase catalytic domain XX DO Adenylyl cyclase VC1, domain C1a XX OS Dog (Canis familiaris) XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // ID D1II7A_ XX EN 1II7 XX TY SCOP XX SI 53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD; XX CL Alpha and beta proteins (a+b) XX FO Metallo-dependent phosphatases XX SF Metallo-dependent phosphatases XX FA DNA double-strand break repair nuclease XX DO Mre11 XX OS Archaeon Pyrococcus furiosus XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // |
Generate DCF file from raw SCOP files. Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-classfile] infile This option specifies the name of raw SCOP classification file dir.cla.scop.txt_X.XX (input). This is the raw SCOP classification file available at http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57. [-desinfile] infile This option specifies the name of raw SCOP description file dir.des.scop.txt_X.XX (input). This is the raw SCOP description file available at http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.57. -nosegments boolean [N] This option specifies whether to omit domains comprising of more than one segment. This is necessary if a continuous residue sequence is required. -nomultichain boolean [N] This option specifies whether to omit domains comprising segments from more than one chain. This is necessary if a continuous residue sequence is required. [-dcffile] outfile [test.scop] This option specifies the name of SCOP DCF file (domain classification file) (output). A 'domain classification file' contains classification and other data for domains from the SCOP or CATH databases. The file is generated by using DOMAINER and is in DCF format (EMBL-like). Domain sequence information can be added to the file by using DOMAINSEQS. Additional (Optional) qualifiers: -nominor boolean [N] This option specifies whether to omit domains from minor classes (defined as anything not in class 'All alpha proteins', 'All beta proteins', 'Alpha and beta proteins (a/b)' or 'Alpha and beta proteins (a+b)'). This is necessary or appropriate for many analyses. Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-dcffile" 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 | ||||
[-classfile] (Parameter 1) |
infile | This option specifies the name of raw SCOP classification file dir.cla.scop.txt_X.XX (input). This is the raw SCOP classification file available at http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57. | Input file | Required |
[-desinfile] (Parameter 2) |
infile | This option specifies the name of raw SCOP description file dir.des.scop.txt_X.XX (input). This is the raw SCOP description file available at http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.57. | Input file | Required |
-nosegments | boolean | This option specifies whether to omit domains comprising of more than one segment. This is necessary if a continuous residue sequence is required. | Boolean value Yes/No | No |
-nomultichain | boolean | This option specifies whether to omit domains comprising segments from more than one chain. This is necessary if a continuous residue sequence is required. | Boolean value Yes/No | No |
[-dcffile] (Parameter 3) |
outfile | This option specifies the name of SCOP DCF file (domain classification file) (output). A 'domain classification file' contains classification and other data for domains from the SCOP or CATH databases. The file is generated by using DOMAINER and is in DCF format (EMBL-like). Domain sequence information can be added to the file by using DOMAINSEQS. | Output file | test.scop |
Additional (Optional) qualifiers | ||||
-nominor | boolean | This option specifies whether to omit domains from minor classes (defined as anything not in class 'All alpha proteins', 'All beta proteins', 'Alpha and beta proteins (a/b)' or 'Alpha and beta proteins (a+b)'). This is necessary or appropriate for many analyses. | Boolean value Yes/No | No |
Advanced (Unprompted) qualifiers | ||||
(none) | ||||
Associated qualifiers | ||||
"-dcffile" associated outfile qualifiers | ||||
-odirectory3 -odirectory_dcffile |
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 |
% scopparse Generate DCF file from raw SCOP files. Raw scop classification file: scop.cla.raw Raw scop description file: scop.des.raw Omit domains comprising of more than one segment. [N]: Y Omit domains comprising segments from more than one chain. [N]: N Domain classification output file [test.scop]: all.scop |
Go to the input files for this example
Go to the output files for this example
FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
SCOP parsable files | SCOP format. | Raw SCOP classification data. | Available from http://scop.mrc-lmb.cam.ac.uk/scop/parse/ | N.A. |
Domain classification file (for SCOP) | DCF format (EMBL-like format for domain classification data). | Classification and other data for domains from SCOP. The file is in DCF format (EMBL-like). | SCOPPARSE | Domain sequence information can be added to the file by using DOMAINSEQS. |
XX AC P02213 XX SP GLB1_SCAIN XX RA 1 START; 146 END; XX SQ SEQUENCE 146 AA; 15947 MW; 5868B4E5 CRC32; PSVYDAAAQL TADVKKDLRD SWKVIGSDKK GNGVALMTTL FADNQETIGY FKRLGDVSQG MANDKLRGHS ITLMYALQNF IDQLDNPDDL VCVVEKFAVN HITRKISAAE FGKINGPIKK VLASKNFGDK YANAWAKLVA VVQAAL XX AC P02213 XX SP GLB1_SCAIN XX RA 1 START; 146 END; XX SQ SEQUENCE 146 AA; 15947 MW; 5868B4E5 CRC32; PSVYDAAAQL TADVKKDLRD SWKVIGSDKK GNGVALMTTL FADNQETIGY FKRLGDVSQG MANDKLRGHS ITLMYALQNF IDQLDNPDDL VCVVEKFAVN HITRKISAAE FGKINGPIKK VLASKNFGDK YANAWAKLVA VVQAAL |
Program name | Description |
---|---|
aaindexextract | Extract amino acid property data from AAINDEX |
allversusall | Sequence similarity data from all-versus-all comparison |
cathparse | Generates DCF file from raw CATH files |
cutgextract | Extract codon usage tables from CUTG database |
domainalign | Generate alignments (DAF file) for nodes in a DCF file |
domainer | Generates domain CCF files from protein CCF files |
domainnr | Removes redundant domains from a DCF file |
domainrep | Reorder DCF file to identify representative structures |
domainseqs | Adds sequence records to a DCF file |
domainsse | Add secondary structure records to a DCF file |
helixturnhelix | Identify nucleic acid-binding motifs in protein sequences |
hetparse | Converts heterogen group dictionary to EMBL-like format |
jaspextract | Extract data from JASPAR |
libgen | Generate discriminating elements from alignments |
matgen3d | Generate a 3D-1D scoring matrix from CCF files |
pdbparse | Parses PDB files and writes protein CCF files |
pdbplus | Add accessibility and secondary structure to a CCF file |
pdbtosp | Convert swissprot:PDB codes file to EMBL-like format |
pepcoil | Predicts coiled coil regions in protein sequences |
printsextract | Extract data from PRINTS database for use by pscan |
prosextract | Processes the PROSITE motif database for use by patmatmotifs |
rebaseextract | Process the REBASE database for use by restriction enzyme applications |
rocon | Generates a hits file from comparing two DHF files |
rocplot | Performs ROC analysis on hits files |
seqalign | Extend alignments (DAF file) with sequences (DHF file) |
seqfraggle | Removes fragment sequences from DHF files |
seqnr | Removes redundancy from DHF files |
seqsort | Remove ambiguous classified sequences from DHF files |
seqwords | Generates DHF files from keyword search of UniProt |
sites | Generate residue-ligand CON files from CCF files |
ssematch | Search a DCF file for secondary structure matches |
tfextract | Process TRANSFAC transcription factor database for use by tfscan |
See also http://emboss.sourceforge.net/