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DOMAINREP documentation
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CONTENTS
1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES
1.0 SUMMARY
Reorder DCF file to identify representative structures
2.0 INPUTS & OUTPUTS
DOMAINREP reads a DCF file (domain classification file) and writes a DCF file containing the same data except that the order of domains within each user-specified node (e.g. family) in the hierarchy may be changed so that the representative structure of each node is given first. The representative structure is found by using stamp and this application must be installed on the system that is running DOMAINREP and correctly configured (see 'Notes' below). A 'domain PDB file' for each domain in the DCF file must exist in a directory specified in the stamp "pdb.directories" file (see 'Notes' below). The domain PDB file contains coordinate data for a single domain from SCOP or CATH, in PDB format. The input and output files are specified by the user.
3.0 INPUT FILE FORMAT
The format of the DCF file is described in the SCOPPARSE documentation.
Input files for usage example
File: all.scop2
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;
//
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4.0 OUTPUT FILE FORMAT
The format of the DCF file is described in the SCOPPARSE documentation.
Output files for usage example
File: all_rep1st.scop
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;
//
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5.0 DATA FILES
DOMAINREP does not use any data files but does make use of the stamp
"pdb.directories" file (see 'Notes').
6.0 USAGE
6.1 COMMAND LINE ARGUMENTS
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. 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
| Standard (Mandatory) qualifiers |
Allowed values |
Default |
[-dcfinfile]
(Parameter 1) |
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 |
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 | (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)) |
|
1 |
[-dcfoutfile]
(Parameter 2) |
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 |
Allowed values |
Default |
| (none) |
| Advanced (Unprompted) qualifiers |
Allowed values |
Default |
| (none) |
6.2 EXAMPLE SESSION
An example of interactive use of DOMAINREP is shown below.
Here is a sample session with domainrep
% 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
stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set > ./domainrep-1234567890.1234.out
stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set > ./domainrep-1234567890.1234.out
stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set > ./domainrep-1234567890.1234.out
stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set > ./domainrep-1234567890.1234.out
stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set > ./domainrep-1234567890.1234.out
stamp -l ./domainrep-1234567890.1234.dom -s -n 2 -slide 5 -prefix ./domainrep-1234567890.1234 -d ./domainrep-1234567890.1234.set > ./domainrep-1234567890.1234.out
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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
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7.0 KNOWN BUGS & WARNINGS
None.
8.0 NOTES
stamp modification
DOMAINREP will only run with with a version of stamp which has been modified
so that PDB id codes of length greater than 4 characters are acceptable.
This involves a trivial change to the stamp module getdomain.c (around line
number 155), a 4 must be changed to a 7 as follows:
temp=getfile(domain[0].id,dirfile,4,OUTPUT);
< change to ... >
temp=getfile(domain[0].id,dirfile,7,OUTPUT);
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stamp configuration
stamp searches for pdb files with a certain prefix, extension and path as
specified in the stamp "pdb.directories" file, which should look like
something like this (change the text according to your system setup):
/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
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None
8.1 GLOSSARY OF FILE TYPES
| 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. |
9.0 DESCRIPTION
The protein structural alignment program stamp aligns multiple structures
to a seed structure. The best alignments will result when the seed is the
best available representative of the entire set, i.e. in
structural terms, is more similar to the other structures than any other
structure.
DOMAINALIGN calls stamp to generate alignments
of domains belonging to the same node (e.g. family) in a DCF file. DOMAINALIGN will produce better
alignments if the DCF file is reordered so that the
representative structure of each node is given first, because the first
strucutres are used as the seeds. The reordering of the DCF file is done by using DOMAINREP.
10.0 ALGORITHM
More information on stamp can be found at
http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/
11.0 RELATED APPLICATIONS
| Program name |
Description |
|---|
| contacts |
Generate intra-chain CON files from CCF files |
| domainalign |
Generate alignments (DAF file) for nodes in a DCF file |
| domainreso |
Remove low resolution domains from a DCF file |
| interface |
Generate inter-chain CON files from CCF files |
| libgen |
Generate discriminating elements from alignments |
| matgen3d |
Generate a 3D-1D scoring matrix from CCF files |
| 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 |
| seqalign |
Extend alignments (DAF file) with sequences (DHF file) |
| seqfraggle |
Removes fragment sequences from DHF files |
| seqsearch |
Generate PSI-BLAST hits (DHF file) from a DAF file |
| seqsort |
Remove ambiguous classified sequences from DHF files |
| seqwords |
Generates DHF files from keyword search of UniProt |
| siggen |
Generates a sparse protein signature from an alignment |
| siggenlig |
Generates ligand-binding signatures from a CON file |
| sigscan |
Generates hits (DHF file) from a signature search |
| sigscanlig |
Searches ligand-signature library & writes hits (LHF file) |
12.0 DIAGNOSTIC ERROR MESSAGES
None.
13.0 AUTHORS
Mat Blades (Matthew.Blades@astrazeneca.com)
Jon Ison (jison@ebi.ac.uk)
The European Bioinformatics Institute
Wellcome Trust Genome Campus
Cambridge CB10 1SD
UK
14.0 REFERENCES
Please cite the authors and EMBOSS.
Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European
Molecular Biology Open Software Suite" Trends in Genetics,
15:276-278.
See also http://emboss.sourceforge.net/
14.1 Other useful references