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PDBTOSP documentation |
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SWISS-PROT Protein Knowledgebase
Swiss Institute of Bioinformatics (SIB); Geneva, Switzerland
European Bioinformatics Institute (EBI); Hinxton, United Kingdom
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Description: Index of Protein Data Bank (PDB) entries referenced in
SWISS-PROT
Name: PDBTOSP.TXT
Release: 40.9 of 31-Jan-2002
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The PDB database is available at the following URL:
USA: http://www.rcsb.org/pdb/
EBI: http://www2.ebi.ac.uk/pdb/
- Number of PDB entries referenced in SWISS-PROT: 9901
- Number of SWISS-PROT entries with one or more pointers to PDB: 3260
PDB Last revision
code date SWISS-PROT entry name(s)
____ ___________ __________________________________________
101M (08-APR-98) : MYG_PHYCA (P02185)
102L (31-OCT-93) : LYCV_BPT4 (P00720)
102M (08-APR-98) : MYG_PHYCA (P02185)
103L (31-OCT-93) : LYCV_BPT4 (P00720)
103M (08-APR-98) : MYG_PHYCA (P02185)
9XIA (15-JUL-92) : XYLA_STRRU (P24300)
9XIM (15-JUL-93) : XYLA_ACTMI (P12851)
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EN 101M XX NE 1 XX IN MYG_PHYCA ID; P02185 ACC; XX // EN 102L XX NE 1 XX IN LYCV_BPT4 ID; P00720 ACC; XX // EN 102M XX NE 1 XX IN MYG_PHYCA ID; P02185 ACC; XX // EN 103L XX NE 1 XX IN LYCV_BPT4 ID; P00720 ACC; XX // EN 103M XX NE 1 XX IN MYG_PHYCA ID; P02185 ACC; XX // EN 9XIA XX NE 1 XX IN XYLA_STRRU ID; P24300 ACC; XX // EN 9XIM XX NE 1 XX IN XYLA_ACTMI ID; P12851 ACC; XX // |
Convert swissprot:PDB codes file to EMBL-like format.
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-infile] infile This option specifies the name of raw
swissprot:PDB equivalence file (input).
HETPARSE parses this file, which is
available at URL
http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt
[-outfile] outfile [Epdbtosp.dat] This option specifies the
name of swissprot:PDB equivalence file
(EMBL-like format). This is the PDBTOSP
output file.
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-outfile" associated qualifiers
-odirectory2 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 | ||||
| [-infile] (Parameter 1) |
infile | This option specifies the name of raw swissprot:PDB equivalence file (input). HETPARSE parses this file, which is available at URL http://www.expasy.ch/cgi-bin/lists?pdbtosp.txt | Input file | Required |
| [-outfile] (Parameter 2) |
outfile | This option specifies the name of swissprot:PDB equivalence file (EMBL-like format). This is the PDBTOSP output file. | Output file | Epdbtosp.dat |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-outfile" associated outfile qualifiers | ||||
| -odirectory2 -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 |
% pdbtosp Convert swissprot:PDB codes file to EMBL-like format. Swissprot:pdb equivalence table file: pdbtosp.txt Swissprot:pdb equivalence output file [Epdbtosp.dat]: |
Go to the input files for this example
Go to the output files for this example
| FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
| swissprot:PDB equivalence file | EMBL-like format. | A file containing swissprot identifiers for PDB codes. | Included in the EMBOSS distribution | N.A. |
| 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 |
| domainer | Generate domain CCF files from protein CCF files |
| domainnr | Remove redundant domains from a DCF file |
| domainseqs | Add sequence records to a DCF file |
| domainsse | Add secondary structure records to a DCF file |
| hetparse | Convert heterogen group dictionary to EMBL-like format |
| jaspextract | Extract data from JASPAR |
| pdbparse | Parse PDB files and writes protein CCF files |
| pdbplus | Add accessibility and secondary structure to a CCF file |
| 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 |
| scopparse | Generate DCF file from raw SCOP files |
| seqnr | Remove redundancy from DHF files |
| 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/