EMBOSS: sigscan

| ## EMBOSS: sigscan

# Program sigscan

## Function

Scans a sparse protein signature against swissprot

## Description

sigscan scans a signature such as that generated by the EMBOSS application siggen against a protein sequence database and generates files of scored hits and corresponding alignments. An (optionally grouped) scop families file can be provided in which case a classification of hits is provided in the signature hits output file. See documentation for the EMBOSS application psiblasts for an explanation of the scop families file and groups for information on how to group it.

### Signatures

Signatures extend the comcept of the motif as a tool for characterizing protein families. They consist of a set of N key residue postitions (A1, A2 ...An) preceeded by gaps (G) thus G1A1G2A2...GnAn. Both a residue and a gap can be variable. A signature is matched to a protein sequence and scored using a dynamic programming algorithm which permits variability in gap distance and residue type. Generating a signature involves identifying residues associated with points of contact in interactions between secondary structure alements. A raw signature consists of a set of positions with potential key structural roles sampled from a sequence alignment constructed with reference to this contact data. Raw signatures are refined by samplinfg different gap-residue pairs until the specificity of a signature for the family cannot be further improved.

## Usage

Here is a sample session with sigscan:

    % sigscan

## Command line arguments

       Mandatory qualifiers:
      [-sigin]             infile     Name of signature file for input
      [-database]          seqall     Name of sequence database to search
      [-targetf]           infile     Name of (optionally grouped) scop families
                                      file for input
      [-thresh]            integer    Minimum length (residues) of overlap
                                      required for two hits with the same code to
                                      be counted as the same hit.
      [-sub]               matrixf    Residue substitution matrix
      [-gapo]              float      The gap insertion penalty is the score taken
                                      away when a gap is created. The best value
                                      depends on the choice of comparison matrix.
                                      The default value assumes you are using the
                                      EBLOSUM62 matrix for protein sequences, and
                                      the EDNAMAT matrix for nucleotide sequences.
      [-gape]              float      The gap extension, penalty is added to the
                                      standard gap penalty for each base or
                                      residue in the gap. This is how long gaps
                                      are penalized. Usually you will expect a few
                                      long gaps rather than many short gaps, so
                                      the gap extension penalty should be lower
                                      than the gap penalty. An exception is where
                                      one or both sequences are single reads with
                                      possible sequencing errors in which case you
                                      would expect many single base gaps. You can
                                      get this result by setting the gap open
                                      penalty to zero (or very low) and using the
                                      gap extension penalty to control gap
                                      scoring.
       -nterm              menu       Select number
      [-nhits]             integer    Number of hits to output
      [-hitsf]             outfile    Name of signature hits file for output
      [-alignf]            outfile    Name of signature alignments file 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
--- | --- | ---
[-sigin] (Parameter 1) | Name of signature file for input | Input file | test.sig
[-database] (Parameter 2) | Name of sequence database to search | Readable sequence(s) | ./test.seq
[-targetf] (Parameter 3) | Name of (optionally grouped) scop families file for input | Input file | test.fam
[-thresh] (Parameter 4) | Minimum length (residues) of overlap required for two hits with the same code to be counted as the same hit. | Any integer value | 20
[-sub] (Parameter 5) | Residue substitution matrix | Comparison matrix file in EMBOSS data path | ./EBLOSUM62
[-gapo] (Parameter 6) | The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAMAT matrix for nucleotide sequences. | Floating point number from 1.0 to 100.0 | 10.0 for any sequence
[-gape] (Parameter 7) | The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. | Floating point number from 0.0 to 10.0 | 0.5 for any sequence
-nterm | Select number |
1 | (Align anywhere and allow only complete signature-sequence fit)
2 | (Align anywhere and allow partial signature-sequence fit)
3 | (Use empirical gaps only)
| 1
[-nhits] (Parameter 8) | Number of hits to output | Any integer value | 100
[-hitsf] (Parameter 9) | Name of signature hits file for output | Output file | test.hits
[-alignf] (Parameter 10) | Name of signature alignments file for output | Output file | test.align
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

Excerpts from a signature hits (Figure 1) are shown. The records used are are as follows:

1. DE - bibliographic information. The text 'Results of signature search' is always given.
2. Four SCOP classification records are given:
   - CL - Domain class. It is identical to the text given after 'Class' in the scop classification file (see documentation for the EMBOSS application scope).
   - FO - Domain fold. It is identical to the text given after 'Fold' in the scop classification file (see scope documentation).
   - SF - Domain superfamily. It is identical to the text given after 'Superfamily' in the scop classification file (see scope documentation).
   - FA - Domain family. It is identical to the text given after 'Family' in the scop classification file (see scope documentation).
3. HI - hit data. The data are as follows (column numbers are given in parentheses).
   - (i) HI is always given.
   - (ii) Rank-order of the hit.
   - (iii) Database identifier code.
   - (iv) The group number of the protein if a grouped scop families file was provided or '.' otherwise.
   - (v) The primary classification of the hit. For true hits (genuine relatives to the signature) one of 'TRAIN', 'PSIBLAST' or 'OTHER' is given. Otherwise, 'CROSS', 'FALSE' or 'UNKNOWN' is given ('.' is given if a scop families file was not provided).
   - (vi) The secondary classification of the hit, either 'FALSE', 'TRUE' or 'UNKNOWN' ('.' is given if a scop families file was not provided). The classes of hits are defined below.
   - (vii) Score of sequence-signature match.
   - (viii) E-value (see below).
4. XX - used for spacing.
5. // - The file ends with a line containing '//' only.

Example excerpt from a signature hits file:

    DE   Results of signature search
    XX
    CL   All alpha proteins
    XX
    FO   Globin-like
    XX
    SF   Globin-like
    XX
    FA   Globins
    XX
    XX
    HI   1    1RBPDFG   1    TRUE     TRUE    234  0.0001
    HI   2    1GFT35J   3    TRUE     TRUE    234  0.0008
    HI   3    1KJUFGH   1    TRUE     TRUE    224  0.0108
    HI   4    1GYU15R   2    CLOSE    TRUE    220  0.1876
    HI   5    1LKI89O   2    CLOSE    TRUE    203  0.6787
    HI   6    1QRTY58   1    TRUE     TRUE    199  0.9978
    HI   7    2IOM78G   1    FALSE    FALSE   198  1.0844
    HI   8    1SZR234   1    CLOSE    TRUE    198  1.4343
    HI   9    3PONI57   1    DISTANT  FALSE   197  2.8849
    HI  10    1PHDJBS   3    CLOSE    TRUE    190  2.9872
    HI  11    1HIOHDW   1    UNKNOWN  UNKNOWN 160  5,8676
    HI  12    199976T   1    CLOSE    TRUE    140  8.8346
    XX
    //

## Output file format

Excerpts from an alignment file are shown (Figure 2). The records used are are as follows:

(1) The DE, CL, FO, SF, FA, XX and // records have the same meaning as in the hits file (above).

(2) Other lines contain either a fragment of protein sequence preceeded by an accession number, or a fragment of an alignment of a signature to the protein sequence (signature positions are marked with a '*'). The two numbers on either side of the sequence are begin and end residue numbers for that line.

Example excerpt from a signature alignment file

    DE   Results of signature search
    XX
    CL   Alpha and beta proteins (a/b)
    XX
    FO   alpha/beta-Hydrolases
    XX
    SF   alpha/beta-Hydrolases
    XX
    FA   Acetylcholinesterase-like
    XX
    OPSD_HUMAN      1        MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMF 45
    SIGNATURE       -        ---------*------------*---------------*------
    OPSD_XENLA      1        MNGTEGPNFYVPMSNKTGVVRSPFDYPQYYLAEPWQYSALAAYMF 45
    SIGNATURE       -        --------*-------------*----------------*-----
    XX
    OPSD_HUMAN      46       LLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGG 90
    SIGNATURE       -        --------------*--------------*------------*--
    OPSD_XENLA      46       LLILLGLPINFMTLFVTIQHKKLRTPLNYILLNLVFANHFMVLCG 90
    SIGNATURE       -        --------------*--------------*------------*--
    XX
    OPSD_HUMAN      91       FTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIER 135
    SIGNATURE       -        ---------*--*--------------------------**----
    OPSD_XENLA      91       FTVTMYTSMHGYFIFGPTGCYIEGFFATLGGEVALWSLVVLAVER 135
    SIGNATURE       -        ---------*----*-------------------------**---
    XX
    //

Definition of classes of hit

The primary classification is an objective definition of the hit and has one of the following values:

TRAIN - the sequence was included in the original alignment from which the signature was generated.

PSIBLAST - A protein which was detected by psiblast (see psiblasts.c) to be a homologue to at least one of the proteins in the family from which the signature was derived. Such proteins are identified by the 'PSIBLAST' record in the scop families file.

OTHER - A true member of the family but not a homologue as detected by psi-blast. Such proteins may have been found from the literature and manually added to the scop families file or may have been detected by the EMBOSS program swissparse (see swissparse.c). They are identified in the

SCOP families file by the 'OTHER' record.

CROSS - A protein which is homologous to a protein of the same fold, but differnt family, of the proteins from which the signature was derived.

FALSE - A homologue to a protein with a different fold to the family of the signature.

UNKNOWN - The protein is not known to be CROSS, FALSE or a true hit (TRAIN, PSIBLAST or OTHER).

The secondary classification is provided for convenience and a value as follows:

Hits of TRAIN, PSIBLAST and OTHER classification are all listed as TRUE.

Hits of CROSS, FALSE or UNKNOWN objective classification are listed as CROSS, FALSE or UNKNOWN respectively.

The subjective column allows for hand-annotation of the hits files so that proteins of UNKNOWN objective classification can re-classified by a human expert as TRUE, FALSE, CROSS or otherwise left as UNKNOWN for the purpose of generating signature performance plots with the EMBOSS application sigplot.

## Data files

None.

## Notes

Important - sigscan presumes that SCOP family names are unique. If this were not the case, changes to ajXyzClassifyHits would have to be made.

Important - In the case where a signature file is generated by hand, it is essential that the gap data given is listed in order of increasing gap size.

## References

Ison JC, Blades MJ, Bleasby AJ, Daniel SC, Parish JH "Key residues approach to the definition of protein families and analysis of sparse family signatures" (2000) PROTEINS: Structure, Function and Genetics 40:330-341

## 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
scopalign | Generate alignments for SCOP families
seqsort | Removes ambiguities from a set of hits resulting from a database search
siggen | Generates a sparse protein signature

## Author(s)

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

## History

Written (July 2001) - Jon Ison

## Target users

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

## Comments