| 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
    Protein pattern search
    Input sequence(s): tsw:*
    Search pattern: [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
    Number of mismatches [0]:
    Output report [100k_rat.fuzzpro]:

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
       -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     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
       -rformat2            string     Report format
       -rname2              string     Base file name
       -rextension2         string     File name extension
       -rdirectory2         string     Output directory
       -raccshow2           boolean    Show accession number in the report
       -rdesshow2           boolean    Show description in the report
       -rscoreshow2         boolean    Show the score in the report
       -rusashow2           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
-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) | Output report file name | Report output file |
Additional (Optional) qualifiers | Allowed values | Default
(none)
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

fuzzpro reads in normal protein sequence USAs.

### Input files for usage example

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

### Pattern specification

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).
- All other characters, including spaces are not allowed.

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 fuzzpro writes a 'seqtable' report file.

### Output files for usage example

### File: 100k_rat.fuzzpro

    ########################################
    # Program: fuzzpro
    # Rundate: Thu Jul 15 2004 12:00:00
    # Report_format: seqtable
    # Report_file: 100k_rat.fuzzpro
    ########################################

    #=======================================
    #
    # Sequence: ACT1_FUGRU     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: ACT2_FUGRU     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: ACT3_FUGRU     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: ACTC_FUGRU     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

    #---------------------------------------
    #---------------------------------------
    #=======================================
    #
    # Sequence: ACTS_FUGRU     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

    #---------------------------------------
    #---------------------------------------
    #=======================================
    #
    # Sequence: ACTT_FUGRU     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

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

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

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)

Alan Bleasby (ableasby © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, 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

None