EMBOSS: fuzzpro

| ## EMBOSS: fuzzpro

# Program fuzzpro

## Function

Protein pattern search

## Description

fuzzpro uses PROSITE style patterns to search protein sequences.

Patterns are specifications of a (typically short) length of sequence to be found. They can specify a search for an exact sequence or they can allow various ambiguities, matches to variable lengths of sequence and repeated subsections of the sequence.

fuzzpro intelligently selects the optimum searching algorithm to use, depending on the complexity of the search pattern specified.

## Usage

Here is a sample session with fuzzpro.

    % fuzzpro
    Input sequence: sw:*
    Search pattern: [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
    Number of mismatches [0]:
    Output file [5h1d_fugru.fuzzpro]:

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
       -pattern            string     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
                                      fuzzpro).
                                      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
                                      fuzzpro).
                                      For example, [DE](2)HS{P}X(2)PX(2,4)C
       -mismatch           integer    Number of mismatches
      [-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
-pattern | 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 fuzzpro). 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 fuzzpro). For example, [DE](2)HS{P}X(2)PX(2,4)C | Any string is accepted | An empty string is accepted
-mismatch | Number of mismatches | Integer 0 or more | 0
[-outfile] (Parameter 2) | (no help text) report value | Report file |
Optional qualifiers | Allowed values | Default
(none)
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

Patterns for fuzzpro 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 fuzzpro).
- 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 fuzzpro).

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 fuzzzpro writes a 'seqtable' report file.

The output from the above example is:

    ########################################
    # Program: fuzzpro
    # Rundate: Thu Apr 11 13:38:06 2002
    # Report_file: 100k_rat.fuzzpro
    ########################################

    #=======================================
    #
    # Sequence: ACT1_ABSGL     from: 1   to: 140
    # HitCount: 1
    #
    # Pattern: [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
    # Mismatch: 0
    #
    #=======================================

      Start     End Mismatch Sequence
         55      65        . YVGDEAQSKRG

    #---------------------------------------
    #---------------------------------------
    #=======================================
    #
    # Sequence: ACT1_ACACA     from: 1   to: 375
    # HitCount: 1
    #
    # Pattern: [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
    # Mismatch: 0
    #
    #=======================================

      Start     End Mismatch Sequence
         53      63        . YVGDEAQSKRG

    #---------------------------------------
    #---------------------------------------
    #=======================================
    #
    # Sequence: ACT1_ARATH     from: 1   to: 377
    # HitCount: 1
    #
    # Pattern: [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
    # Mismatch: 0
    #
    #=======================================

      Start     End Mismatch Sequence
         55      65        . YVGDEAQSKRG

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

    etc.

## Data files

None.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with a status of 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
antigenic | Finds antigenic sites in proteins
digest | Protein proteolytic enzyme or reagent cleavage digest
fuzztran | Protein pattern search after translation
helixturnhelix | Report nucleic acid binding motifs
oddcomp | Finds protein sequence regions with a biased composition
patmatdb | Search a protein sequence with a motif
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

- fuzznuc - Nucleic acid pattern search
- fuzztran - Protein pattern search after translation

Other EMBOSS programs allow you to search for regular expression patterns but may be less easy for the user who has never used regular expressions before:

- dreg - Regular expression search of a nucleotide sequence
- preg - Regular expression search of a protein sequence

## Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

## History

Written (2000) - Alan Bleasby
'-usa' added (13 March 2001) - Gary Williams

## Target users

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

## Comments