CATHPARSE documentation |
1cuk03 1 10 8 10 1 1 1 48 1.900 1hjp03 1 10 8 10 1 1 2 44 2.500 |
1cuk00 D03 F00 1 0 1 - 0 66 - 1 0 67 - 0 142 - 1 0 156 - 0 203 - 1hjp00 D03 F01 1 0 1 - 0 66 - 1 0 67 - 0 158 - 1 0 159 - 0 202 - 0 203 - 0 203 - (1) |
1.10.8 1cuk03 :Helicase, Ruva Protein, domain 3 1.10.8.10 1cuk03 :DNA helicase RuvA subunit, C-terminal domain 0001 2ccyA0 :Mainly Alpha 0001.0010 1eca00 :Orthogonal Bundle |
ID 1CUK03 XX EN 1CUK XX TY CATH XX CI 1 CL; 10 AR; 8 TP; 10 SF; 1 FA; 1 NI;1 IF; XX CL Mainly Alpha XX AR Orthogonal Bundle XX TP Helicase, Ruva Protein, domain 3 XX SF DNA helicase RuvA subunit, C-terminal domain XX NR 48 XX NC 1 XX CN [1] XX CH 0 CHAIN; 156 START; 203 END; // ID 1HJP03 XX EN 1HJP XX TY CATH XX CI 1 CL; 10 AR; 8 TP; 10 SF; 1 FA; 1 NI;2 IF; XX CL Mainly Alpha XX AR Orthogonal Bundle XX TP Helicase, Ruva Protein, domain 3 XX SF DNA helicase RuvA subunit, C-terminal domain XX NR 44 XX NC 1 XX CN [1] XX CH 0 CHAIN; 159 START; 202 END; // |
1.10.8.10 1.10.8 0001.0010 0001 1.10.8.10 1.10.8 0001.0010 0001 |
Generates DCF file from raw CATH files. Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-listfile] infile [caths.list.v2.4] This option specifies the name of raw CATH classification file (caths.list.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). [-domfile] infile [domlist.v2.4] This option specifies the name of raw CATH classification file (domlist.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). [-namesfile] infile [CAT.names.all.v2.4] This option specifies the name of raw CATH classification file (CAT.names.all.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). [-outfile] outfile [Ecath.dat] This option specifies the name of CATH DCF file (domain classification file) (output). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS. -logfile outfile [cathparse.log] This option specifies the name of the CATHPARSE log file. Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-outfile" associated qualifiers -odirectory4 string Output directory "-logfile" associated qualifiers -odirectory 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 | ||||
[-listfile] (Parameter 1) |
infile | This option specifies the name of raw CATH classification file (caths.list.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). | Input file | caths.list.v2.4 |
[-domfile] (Parameter 2) |
infile | This option specifies the name of raw CATH classification file (domlist.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). | Input file | domlist.v2.4 |
[-namesfile] (Parameter 3) |
infile | This option specifies the name of raw CATH classification file (CAT.names.all.vX.X) (input). The raw CATH parsable files (classification and description files) available from ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4). | Input file | CAT.names.all.v2.4 |
[-outfile] (Parameter 4) |
outfile | This option specifies the name of CATH DCF file (domain classification file) (output). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS. | Output file | Ecath.dat |
-logfile | outfile | This option specifies the name of the CATHPARSE log file. | Output file | cathparse.log |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
(none) | ||||
Associated qualifiers | ||||
"-outfile" associated outfile qualifiers | ||||
-odirectory4 -odirectory_outfile |
string | Output directory | Any string | |
"-logfile" associated outfile qualifiers | ||||
-odirectory | 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 |
% cathparse Generates DCF file from raw CATH files. Raw cath list file [caths.list.v2.4]: caths.list.small Raw cath domlist file [domlist.v2.4]: domlist.small Raw cath names file [CAT.names.all.v2.4]: CAT.names.all.small Domain classification output file [Ecath.dat]: Domainatrix log output file [cathparse.log]: |
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FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
SCOP parsable files | CATH format. | Raw CATH classification data. | Available from ftp.biochem.ucl.ac.uk (e.g. /pub/cathdata/v2.4) | N.A. |
Domain classification file (for CATH) | DCF format (EMBL-like). | Classification and other data for domains from CATH. | CATHPARSE | Domain sequence information can be added to the file by using DOMAINSEQS. |
Program name | Description |
---|---|
aaindexextract | Extract amino acid property data from AAINDEX |
allversusall | Sequence similarity data from all-versus-all comparison |
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 |
scopparse | Generate DCF file from raw SCOP 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/