EMBOSS: stamps


Program stamps

Function

Generate alignments for SCOP families

Description

stamps parses a SCOP classification file in EMBL-like format generated by the EMBOSS applications scope or nrscope, and domain coordinate files generated by the EMBOSS application domainer, and calls stamp to generate structural alignments for each SCOP family in turn.

VERY IMPORTANT NOTE

stamps 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);
temp=getfile(domain[0].id,dirfile,7,OUTPUT);

The modified code is kept on the HGMP file system in /packages/stamp/src2 WHEN RUNNING STAMPS AT THE HGMP IT IS ESSENTIAL THAT THE COMMAND 'use stamp2' (which runs the script /packages/menu/USE/stamp2) IS GIVEN BEFORE STAMPS IS RUN. This will ensure that the modified version of stamp is used.

Usage

Here is a sample session with stamps:

% stamps

Command line arguments

   Mandatory qualifiers:
  [-scopf]             infile     Name of scop file for input (embl-like
                                  format)
  [-path]              string     Location of alignment files for output

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


Mandatory qualifiers Allowed values Default
[-scopf]
(Parameter 1)
Name of scop file for input (embl-like format) Input file Escop.dat
[-path]
(Parameter 2)
Location of alignment files for output Any string is accepted ./
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
(none)

Input file format

Output file format

The names of the output files are identical to the names of the families given in the SCOP classification records, except that if a file of a certain name already exists, then an "_1", "_2" etc will be added as appropriate.

The format of the stamps output file (Figure 1) is similar to the output file generated by stamp when issued with the following three types of command:

(1) stamp -l ./stamps_file.dom -s -n 2 -slide 5 -prefix ./stamps_file -d ./stamps_file.set;sorttrans -f ./stamps_file.scan -s Sc 2.5 > ./stamps_file.sort;stamp -l ./stamps_file.sort -prefix ./stamps_file > ./stamps_file.log

(2) poststamp -f ./stamps_file.3 -min 0.5

(3) ver2hor -f ./stamps_file.3.post > ./stamps_file.out

However, the SCOP classification records for the appopriate family are written above the alignment, no dssp assignments are given, and only the 'Post similar' line is given. Also, 7 character domain identifier codes taken from the scop classificaiton file are given.

Figure 1 Example of stamps output file

 CL   All alpha proteins
 XX
 FO   Globin-like
 XX
 SF   Globin-like
 XX
 FA   Globins
 XX
 Number               10        20        30        40        50    
 d1vrea_              LSAAQRQVVASTWKDIAgsdngAGVGKECFTKFLSAHHDMAAV f gFS
 d3sdhb_      svydaaaqLTADVKKDLRDSWKVIG sd kKGNGVALMTTLFADNQETIGYfkrlGN
 d3hbia_      svydaaaqLTADVKKDLRDSWKVIG sd kKGNGVALMTTLFADNQETIGYfkrlGN
 d3sdha_      svydaaaqLTADVKKDLRDSWKVIG sd kKGNGVALMTTLFADNQETIGYfkrlGN
 Post_similar --------11111111111111111-00-1111111111111111111111-0-111
 
 Number        60        70        80        90       100       110 
 d1vrea_      GAS   dpGVADLGAKVLAQIGVAVSHLgDEGKMVAEMKAVGVRHKgygnkhIKAEY
 d3sdhb_      VSQgmandKLRGHSITLMYALQNFIDQLdNPDDLVCVVEKFAVNHI  t rkISAAE
 d3hbia_      VSQgmandKLRGHSITLMYALQNFIDQLdNPDDLVCVVEKLAVNHI  t rkISAAE
 d3sdha_      VSQgmandKLRGHSITLMYALQNFIDQLdNPDDLVCVVEKFAVNHI  t rkISAAE
 Post_similar 111---0011111111111111111111011111111111111111--0-0011111
 
 Number          120       130       140       150       160
 d1vrea_      FEPlGASL LSAMEhriggkMNAAAKDAWAAAYADisgalisglqs
 d3sdhb_      FGK INGPiKKVLA s k nFGDKYANAWAKLVAVvqa al     
 d3hbia_      FGK INGPiKKVLA s k nFGDKYANAWAKLVAVvqa al     
 d3sdha_      FGK INGPiKKVLA s k nFGDKYANAWAKLVAVvqa al     
 Post_similar 111-1111-11111-0-0-1111111111111111100-00-----

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
scopalignGenerate alignments for SCOP families

Author(s)

This application was written by Jon Ison (jison@hgmp.mrc.ac.uk)

History

Written (May 2001) - Jon Ison

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments