| 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): tsw:*
    Protein motif to search for: st[ty]s
    Output report [100k_rat.patmatdb]:

Go to the input files for this example
Go to the output files for this example

## Command line arguments

       Standard (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     Output report file name

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1             integer    Start of each sequence to be used
       -send1               integer    End of each sequence to be used
       -sreverse1           boolean    Reverse (if DNA)
       -sask1               boolean    Ask for begin/end/reverse
       -snucleotide1        boolean    Sequence is nucleotide
       -sprotein1           boolean    Sequence is protein
       -slower1             boolean    Make lower case
       -supper1             boolean    Make upper case
       -sformat1            string     Input sequence format
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name

       "-outfile" associated qualifiers
       -rformat3            string     Report format
       -rname3              string     Base file name
       -rextension3         string     File name extension
       -rdirectory3         string     Output directory
       -raccshow3           boolean    Show accession number in the report
       -rdesshow3           boolean    Show description in the report
       -rscoreshow3         boolean    Show the score in the report
       -rusashow3           boolean    Show the full USA in the report

       General qualifiers:
       -auto                boolean    Turn off prompts
       -stdout              boolean    Write standard output
       -filter              boolean    Read standard input, write 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 deaths

Standard (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) | Output report file name | Report output file |
Additional (Optional) qualifiers | Allowed values | Default
(none)
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

patmatdb reads in one or more protein sequence USAs.

### Input files for usage example

'tsw:*' is a sequence entry in the example protein database 'tsw'

### Pattern specification

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://emboss.sf.net/docs/themes/ReportFormats.html for further information on report formats.

By default patmatdb writes a 'dbmotif' report file.

### Output files for usage example

### File: 100k_rat.patmatdb

    ########################################
    # Program: patmatdb
    # Rundate: Thu Jul 15 2004 12:00:00
    # Report_format: dbmotif
    # Report_file: 100k_rat.patmatdb
    ########################################

    #=======================================
    #
    # Sequence: HD_FUGRU     from: 1   to: 3148
    # HitCount: 1
    #
    # Motif: ST[TY]S
    #
    #=======================================

    Length = 4
    Start = position 1038 of sequence
    End = position 1041 of sequence

    STPASSTTSSAVDP
         |  |
      1038  1041

    #---------------------------------------
    #---------------------------------------
    #=======================================
    #
    # Sequence: GCN4_YEAST     from: 1   to: 281
    # HitCount: 1
    #
    # Motif: ST[TY]S
    #
    #=======================================

    Length = 4
    Start = position 158 of sequence
    End = position 161 of sequence

    SNLEVSTTSFLPTP
         |  |
       158  161

    #---------------------------------------
    #---------------------------------------
    #=======================================
    #
    # Sequence: PAXI_HUMAN     from: 1   to: 557
    # HitCount: 1
    #
    # Motif: ST[TY]S
    #
    #=======================================

    Length = 4
    Start = position 13 of sequence
    End = position 16 of sequence

    LADLESTTSHISKR
         |  |
        13  16

    #---------------------------------------
    #---------------------------------------

## 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
epestfind | Finds PEST motifs as potential proteolytic cleavage sites
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

## Author(s)

Sinead O'Leary (current e-mail address unknown)
while she was at:
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, 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

None