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DOMAINSSE documentation |
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; // |
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
SE HH
XX
SS SEQUENCE 46 AA; 6039 MW; 32D7FC5C51294C12 CRC64;
LLLHHHHHHH LLHHHHHHHH HHHHHHHHHH HHHHHLLEEE EEELLL
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
SE HEEE
XX
SS SEQUENCE 43 AA; 5411 MW; F2A5FA03304F5F35 CRC64;
LLLLLLHHHH EEEEEEEEEE EEEEEEEEEE EELLLEEEEE LLL
XX
NC 1
XX
CN [1]
XX
CH A CHAIN; . START; . END;
//
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Add secondary structure records to a DCF file.
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-dcfinfile] infile This option specifies the name of the DCF
file (domain classification file) (input). 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.
[-dccfdir] directory [./] This option specifies the location of
the domain CCF file (clean coordinate files)
(input). A 'clean cordinate file' contains
protein coordinate and derived data for a
single PDB file ('protein clean coordinate
file') or a single domain from SCOP or CATH
('domain clean coordinate file'), in CCF
format (EMBL-like). The files, generated by
using PDBPARSE (PDB files) or DOMAINER
(domains), contain 'cleaned-up' data that is
self-consistent and error-corrected.
Records for residue solvent accessibility
and secondary structure are added to the
file by using PDBPLUS.
[-dcfoutfile] outfile [*.domainsse] This option specifies the name
of the DCF file (domain classification
file) with secondary structure records
(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 [domainsse.log] This option specifies the
name of the DOMAINSSE log file.
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-dccfdir" associated qualifiers
-extension2 string Default file extension
"-dcfoutfile" associated qualifiers
-odirectory3 string Output directory
"-logfile" associated qualifiers
-odirectory4 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 | ||||
| [-dcfinfile] (Parameter 1) |
infile | This option specifies the name of the DCF file (domain classification file) (input). 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. | Input file | Required |
| [-dccfdir] (Parameter 2) |
directory | This option specifies the location of the domain CCF file (clean coordinate files) (input). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. | Directory | ./ |
| [-dcfoutfile] (Parameter 3) |
outfile | This option specifies the name of the DCF file (domain classification file) with secondary structure records (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 | <*>.domainsse |
| [-logfile] (Parameter 4) |
outfile | This option specifies the name of the DOMAINSSE log file. | Output file | domainsse.log |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-dccfdir" associated directory qualifiers | ||||
| -extension2 -extension_dccfdir |
string | Default file extension | Any string | ccf |
| "-dcfoutfile" associated outfile qualifiers | ||||
| -odirectory3 -odirectory_dcfoutfile |
string | Output directory | Any string | |
| "-logfile" associated outfile qualifiers | ||||
| -odirectory4 -odirectory_logfile |
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 |
% domainsse Add secondary structure records to a DCF file. Domain classification file: ../scopparse-keep/all.scop Clean domain coordinates directory [./]: ../domainer-domainatrix Domain classification output file [all.domainsse]: domainsse.out Domainatrix log output file [domainsse.log]: domainsse.log Processing D1CS4A_ Processing D1II7A_ Done! output file name: domainsse.out log file name: domainsse.log |
Go to the input files for this example
Go to the output files for this example
| FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
| Domain classification file (for SCOP) | DCF format (EMBL-like format for domain classification data). | Classification and other data for domains from SCOP. | SCOPPARSE | Domain sequence information can be added to the file by using DOMAINSEQS. |
| Domain classification file (for CATH) | DCF format (EMBL-like format for domain classification data). | Classification and other data for domains from CATH. | CATHPARSE | Domain sequence information can be added to the file by using DOMAINSEQS. |
| Clean coordinate file (for protein) | CCF format (EMBL-like format for protein coordinate and derived data). | Coordinate and other data for a single PDB file. The data are 'cleaned-up': self-consistent and error-corrected. | PDBPARSE | Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. |
| Clean coordinate file (for domain) | CCF format (EMBL-like format for protein coordinate and derived data). | Coordinate and other data for a single domain from SCOP or CATH. The data are 'cleaned-up': self-consistent and error-corrected. | DOMAINER | Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. |
| Program name | Description |
|---|---|
| aaindexextract | Extract amino acid property data from AAINDEX |
| allversusall | Sequence similarity data from all-versus-all comparison |
| cathparse | Generate 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 | Generate domain CCF files from protein CCF files |
| domainnr | Remove redundant domains from a DCF file |
| domainrep | Reorder DCF file to identify representative structures |
| domainseqs | Add sequence records to a DCF file |
| helixturnhelix | Identify nucleic acid-binding motifs in protein sequences |
| hetparse | Convert 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 | Parse 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 | Predict coiled coil regions in protein sequences |
| printsextract | Extract data from PRINTS database for use by pscan |
| prosextract | Process the PROSITE motif database for use by patmatmotifs |
| rebaseextract | Process the REBASE database for use by restriction enzyme applications |
| rocon | Generate a hits file from comparing two DHF files |
| rocplot | Perform ROC analysis on hits files |
| scopparse | Generate DCF file from raw SCOP files |
| seqalign | Extend alignments (DAF file) with sequences (DHF file) |
| seqfraggle | Remove fragment sequences from DHF files |
| seqnr | Remove redundancy from DHF files |
| seqsort | Remove ambiguous classified sequences from DHF files |
| seqwords | Generate 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/