EMBOSS: patmatdb

| ## EMBOSS: patmatdb

# Program patmatdb

## Function

Search a protein sequence with a motif

## Description

Takes a protein motif and compares it to a set of protein sequences.

It returns the number of matches there were between the motif and each matched sequence, length of match, start and end positions of match, and writes out an alignment.

## Usage

Here is a sample session with patmatdb.

    % patmatdb
    Search a protein sequence with a motif
    Input sequence(s): sw:*
    Protein motif to search for: st[ty]s
    Output file [5h1d_fugru.patmatdb]:

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
      [-motif]             string     Patterns for patmatdb are based on the
                                      format of pattern used in the PROSITE
                                      database. For example:
                                      '[DE](2)HS{P}X(2)PX(2,4)C' means two Asps or
                                      Glus in any order followed by His, Ser, any
                                      residue other then Pro, then two of any
                                      residue followed by Pro followed by two to
                                      four of any residue followed by Cys. The
                                      search is case-independent, so 'AAA' matches
                                      'aaa'.
      [-outfile]           report     (no help text) report value

       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
--- | --- | ---
[-sequence] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
[-motif] (Parameter 2) | Patterns for patmatdb are based on the format of pattern used in the PROSITE database. For example: '[DE](2)HS{P}X(2)PX(2,4)C' means two Asps or Glus in any order followed by His, Ser, any residue other then Pro, then two of any residue followed by Pro followed by two to four of any residue followed by Cys. The search is case-independent, so 'AAA' matches 'aaa'. | A string of at least 2 characters | Required
[-outfile] (Parameter 3) | (no help text) report value | Report file |
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

It reads in one or more protein sequences.

Patterns for patmatdb are based on the format of pattern used in the PROSITE database, with the difference that the terminating dot '.' and the hyphens, '-', between the characters are optional.

The PROSITE pattern definition from the PROSITE documentation follows.

- The standard IUPAC one-letter codes for the amino acids are used.
- The symbol `x' is used for a position where any amino acid is accepted.
- Ambiguities are indicated by listing the acceptable amino acids for a given position, between square parentheses `[ ]'. For example: [ALT] stands for Ala or Leu or Thr.
- Ambiguities are also indicated by listing between a pair of curly brackets `{ }' the amino acids that are not accepted at a given position. For example: {AM} stands for any amino acid except Ala and Met.
- Each element in a pattern is separated from its neighbor by a `-'. (Optional in patmatdb).
- Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis. Examples: x(3) corresponds to x-x-x, x(2,4) corresponds to x-x or x-x-x or x-x-x-x.
- When a pattern is restricted to either the N- or C-terminal of a sequence, that pattern either starts with a `<' symbol or respectively ends with a `>' symbol.
- A period ends the pattern. (Optional in patmatdb).

For example, in SWISSPROT entry 100K_RAT you can look for the pattern:

    [DE](2)HS{P}X(2)PX(2,4)C

This means: Two Asps or Glus in any order followed by His, Ser, any residue other then Pro, then two of any residue followed by Pro followed by two to four of any residue followed by Cys.

The search is case-independent, so 'AAA' matches 'aaa'.

## Output file format

The output is a standard EMBOSS report file.

The results can be output in one of several styles by using the command-line qualifier -rformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: embl, genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel, feattable, motif, regions, seqtable, simple, srs, table, tagseq

See: http://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for further information on report formats.

By default patmatdb writes a 'dbmotif' report file.

The output from the above example follows:

    ########################################
    # Program: patmatdb
    # Rundate: Thu Apr 11 13:56:31 2002
    # Report_file: 5h1d_fugru.patmatdb
    ########################################

    #=======================================
    #
    # Sequence: 2AAA_YEAST     from: 1   to: 635
    # HitCount: 2
    #
    # Motif: ST[TY]S
    #
    #=======================================

    Length = 4
    Start = position 19 of sequence
    End = position 22 of sequence

    SAATTSTTSTTSNS
         |  |
        19  22

    Length = 4
    Start = position 22 of sequence
    End = position 25 of sequence

    TTSTTSTTSNSKDS
         |  |
        22  25

    #---------------------------------------
    #---------------------------------------
    #=======================================
    #
    # Sequence: 41_XENLA     from: 1   to: 801
    # HitCount: 1
    #
    # Motif: ST[TY]S
    #
    #=======================================

    Length = 4
    Start = position 52 of sequence
    End = position 55 of sequence

    SQESPSTTSPSTRK
         |  |
        52  55

    etc.

## Data files

None.

## Notes

None.

## References

1. Bairoch, A., Bucher P. (1994) PROSITE: recent developments. Nucleic Acids Research, Vol 22, No.17 3583-3589.
2. Bairoch, A., (1992) PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Research, Vol 20, Supplement, 2013-2018.
3. Peek, J., O'Reilly, T., Loukides, M., (1997) Unix Power Tools, 2nd Edition.
4. Gusfield, D., (1997) Algorithms on strings, Trees and Sequences.
5. Sedgewick, R,. (1990) Algorithms in C.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0

## Known bugs

None.

## See also

Program name | Description
--- | ---
antigenic | Finds antigenic sites in proteins
digest | Protein proteolytic enzyme or reagent cleavage digest
fuzzpro | Protein pattern search
fuzztran | Protein pattern search after translation
helixturnhelix | Report nucleic acid binding motifs
oddcomp | Finds protein sequence regions with a biased composition
patmatmotifs | Search a PROSITE motif database with a protein sequence
pepcoil | Predicts coiled coil regions
preg | Regular expression search of a protein sequence
pscan | Scans proteins using PRINTS
sigcleave | Reports protein signal cleavage sites

fuzzpro - Protein pattern search
This does much the same is patmatdb, but has a slightly different style of output and allows mismatches.

patmatmotifs - Compares a protein sequence to the PROSITE motif database.
This does the opposite to patmatdb, comparing a database of motifs to one sequence.

## Author(s)

This application was written by Sinead O'Leary (soleary@hgmp.mrc.ac.uk)

## History

Completed April 30 1999.

## Target users

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

## Comments