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DOMAINREP 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 D1FX2A_ XX EN 1FX2 XX TY SCOP XX SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55081 DO; 55082 SO; 39430 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 Receptor-type monomeric adenylyl cyclase XX OS Trypanosome (Trypanosoma brucei), different isoform XX NC 1 XX CN [1] XX [Part of this file has been deleted for brevity] XX EN 4AT1 XX TY SCOP XX SI 53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39019 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX DO Aspartate carbamoyltransferase XX OS Escherichia coli XX NC 1 XX CN [1] XX CH B CHAIN; 8 START; 100 END; // ID D4AT1D1 XX EN 4AT1 XX TY SCOP XX SI 53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39020 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX DO Aspartate carbamoyltransferase XX OS Escherichia coli XX NC 1 XX CN [1] XX CH D CHAIN; 8 START; 100 END; // |
ID D4AT1B1 XX EN 4AT1 XX TY SCOP XX SI 53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39019 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX DO Aspartate carbamoyltransferase XX OS Escherichia coli XX NC 1 XX CN [1] XX CH B CHAIN; 8 START; 100 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 NC 1 XX CN [1] XX [Part of this file has been deleted for brevity] XX EN 1FX2 XX TY SCOP XX SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55081 DO; 55082 SO; 39430 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 Receptor-type monomeric adenylyl cyclase XX OS Trypanosome (Trypanosoma brucei), different isoform XX NC 1 XX CN [1] XX CH A CHAIN; . START; . END; // ID D4AT1D1 XX EN 4AT1 XX TY SCOP XX SI 53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39020 DD; XX CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX DO Aspartate carbamoyltransferase XX OS Escherichia coli XX NC 1 XX CN [1] XX CH D CHAIN; 8 START; 100 END; // |
Reorder DCF file to identify representative structures.
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-dcfinfile] infile This option specifies the name of 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.
-node menu [1] This option specifies the node fore
reordering the file. Reordering can be done
for any specified node in the SCOP or CATH
hierarchies. For example by selecting
'Class' entries belonging to the same Class
will be reordered in turn. (Values: 1 (Class
(SCOP)); 2 (Fold (SCOP)); 3 (Superfamily
(SCOP)); 4 (Family (SCOP)); 5 (Class
(CATH)); 6 (Architecture (CATH)); 7
(Topology (CATH)); 8 (Homologous Superfamily
(CATH)); 9 (Family (CATH)))
[-dcfoutfile] outfile [test.scop] This option specifies the name
of 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.
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-dcfoutfile" 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 | ||||||||||||||||||||||
| [-dcfinfile] (Parameter 1) |
infile | This option specifies the name of 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 | ||||||||||||||||||
| -node | list | This option specifies the node fore reordering the file. Reordering can be done for any specified node in the SCOP or CATH hierarchies. For example by selecting 'Class' entries belonging to the same Class will be reordered in turn. |
|
1 | ||||||||||||||||||
| [-dcfoutfile] (Parameter 2) |
outfile | This option specifies the name of 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 | test.scop | ||||||||||||||||||
| Additional (Optional) qualifiers | ||||||||||||||||||||||
| (none) | ||||||||||||||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||||||||||||||
| (none) | ||||||||||||||||||||||
| Associated qualifiers | ||||||||||||||||||||||
| "-dcfoutfile" associated outfile qualifiers | ||||||||||||||||||||||
| -odirectory2 -odirectory_dcfoutfile |
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 | ||||||||||||||||||
% domainrep
Reorder DCF file to identify representative structures.
Domain classification file: all.scop2
Node at which to reorder
1 : Class (SCOP)
2 : Fold (SCOP)
3 : Superfamily (SCOP)
4 : Family (SCOP)
5 : Class (CATH)
6 : Architecture (CATH)
7 : Topology (CATH)
8 : Homologous Superfamily (CATH)
9 : Family (CATH)
Select number. [1]: 2
Domain classification output file [test.scop]: all_rep1st.scop
/shared/software/bin/stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set
/shared/software/bin/stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set
/shared/software/bin/stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set
/shared/software/bin/stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set
/shared/software/bin/stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set
/shared/software/bin/stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set
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Go to the input files for this example
Go to the output files for this example
The following command line would achieve the same result.
domainrep test_data/all.scop test_data/domainrep/all_rep1st.scop -node 4 |
temp=getfile(domain[0].id,dirfile,4,OUTPUT); < change to ... > temp=getfile(domain[0].id,dirfile,7,OUTPUT); |
/data/pdb - - /data/pdb _ .ent /data/pdb _ .pdb /data/pdb pdb .ent /data/pdbscop _ _ /data/pdbscop _ .ent /data/pdbscop _ .pdb /data/pdbscop pdb .ent ./ _ _ ./ _ .ent ./ _ .ent.z ./ _ .ent.gz ./ _ .pdb ./ _ .pdb.Z ./ _ .pdb.gz ./ pdb .ent ./ pdb .ent.Z ./ pdb .ent.gz /data/CASS1/pdb/coords/ _ .pdb /data/CASS1/pdb/coords/ _ .pdb.Z /data/CASS1/pdb/coords/ _ .pdb.gz |
| 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. |
| Domain PDB file | PDB format for domain coordinate data. | Coordinate data for a single domain from SCOP or CATH. | DOMAINER | N.A. |
| Program name | Description |
|---|---|
| cathparse | Generates DCF file from raw CATH files |
| contacts | Generate intra-chain CON files from CCF files |
| domainalign | Generate alignments (DAF file) for nodes in a DCF file |
| domainnr | Removes redundant domains from a DCF file |
| domainreso | Remove low resolution domains from a DCF file |
| 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 |
| interface | Generate inter-chain CON files from CCF files |
| libgen | Generate discriminating elements from alignments |
| matcher | Waterman-Eggert local alignment of two sequences |
| matgen3d | Generate a 3D-1D scoring matrix from CCF files |
| oalistat | Statistics for multiple alignment files |
| pepcoil | Predicts coiled coil regions in protein sequences |
| psiphi | Calculates phi and psi torsion angles from protein coordinates |
| 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 |
| seqmatchall | All-against-all word comparison of a sequence set |
| seqsort | Remove ambiguous classified sequences from DHF files |
| seqwords | Generates DHF files from keyword search of UniProt |
| ssematch | Search a DCF file for secondary structure matches |
| supermatcher | Calculate approximate local pair-wise alignments of larger sequences |
| water | Smith-Waterman local alignment of sequences |
| wordfinder | Match large sequences against one or more other sequences |
| wordmatch | Finds regions of identity (exact matches) of two sequences |
See also http://emboss.sourceforge.net/