| ## EMBOSS: scopalign

# Program scopalign

## Function

Generate alignments for SCOP families

## Description

scopalign 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

scopalign 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 SCOPALIGN AT THE HGMP IT IS ESSENTIAL THAT THE COMMAND 'use stamp2' (which runs the script /packages/menu/USE/stamp2) IS GIVEN BEFORE SCOPALIGN IS RUN. This will ensure that the modified version of stamp is used.

## Usage

Here is a sample session with scopalign:

    % scopalign

## 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

scopalign 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.

## 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 scopalign 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 scopalign 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

scopalign 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 SCOPALIGN AT THE HGMP IT IS ESSENTIAL THAT THE COMMAND 'use stamp2' (which runs the script /packages/menu/USE/stamp2) IS GIVEN BEFORE SCOPALIGN IS RUN. This will ensure that the modified version of stamp is used.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
contacts | Reads coordinate files and writes contact files
dichet | Parse dictionary of heterogen groups
interface | Reads coordinate files and writes inter-chain contact files
psiblasts | Runs PSI-BLAST given scopalign alignments
seqsort | Removes ambiguities from a set of hits resulting from a database search
siggen | Generates a sparse protein signature
sigscan | Scans a sparse protein signature against swissprot

## 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