EMBOSS: fuzzpro

| fuzzpro

## Function

Search for patterns in protein sequences

## Description

fuzznuc searches for a specified PROSITE-style pattern in protein sequences. Such 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. One or more protein sequences are read from file. The output is a standard EMBOSS report file that includes data such as location and score of any matches.

## Algorithm

fuzznuc 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
    Search for patterns in protein sequences
    Input protein sequence(s): tsw:*
    Search pattern: [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
    Output report [edd1_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     Protein sequence(s) filename and optional
                                      format, or reference (input USA)
       -pattern            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
      [-outfile]           report     [*.fuzzpro] 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

       "-pattern" associated qualifiers
       -pformat            string     File format
       -pmismatch          integer    Pattern mismatch
       -pname              string     Pattern base 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
       -rstrandshow2       boolean    Show the nucleotide strand in the report
       -rusashow2          boolean    Show the full USA in the report
       -rmaxall2           integer    Maximum total hits to report
       -rmaxseq2           integer    Maximum hits to report for one sequence

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to 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 dying program messages

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Protein sequence(s) filename and optional format, or reference (input 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 | Property value(s) |
[-outfile] (Parameter 2) | Output report file name | Report output file | <*>.fuzzpro
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: edd1_rat.fuzzpro

    ########################################
    # Program: fuzzpro
    # Rundate: Tue 15 Jul 2008 12:00:00
    # Commandline: fuzzpro
    #    -sequence "tsw:*"
    #    -pattern "[FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G"
    # Report_format: seqtable
    # Report_file: edd1_rat.fuzzpro
    ########################################

    #=======================================
    #
    # Sequence: ACTB1_FUGRU     from: 1   to: 375
    # HitCount: 1
    #
    # Pattern_name Mismatch Pattern
    # pattern1            0 [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
    #
    #=======================================

      Start     End Pattern_name Mismatch Sequence
         53      63 pattern1            . YVGDEAQSKRG

    #---------------------------------------
    #---------------------------------------
    #=======================================
    #
    # Sequence: ACTB_OREMO     from: 1   to: 375
    # HitCount: 1
    #
    # Pattern_name Mismatch Pattern
    # pattern1            0 [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
    #
    #=======================================

      Start     End Pattern_name Mismatch Sequence
         53      63 pattern1            . YVGDEAQSKRG

    #---------------------------------------
    #---------------------------------------
    #=======================================
    #
    # Sequence: ACTB2_FUGRU     from: 1   to: 375
    # HitCount: 1
    #
    # Pattern_name Mismatch Pattern
    # pattern1            0 [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
    #
    #=======================================

      [Part of this file has been deleted for brevity]

    #---------------------------------------
    #=======================================
    #
    # Sequence: ACTSA_FUGRU     from: 1   to: 377
    # HitCount: 1
    #
    # Pattern_name Mismatch Pattern
    # pattern1            0 [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
    #
    #=======================================

      Start     End Pattern_name Mismatch Sequence
         55      65 pattern1            . YVGDEAQSKRG

    #---------------------------------------
    #---------------------------------------
    #=======================================
    #
    # Sequence: ACTS_OREMO     from: 1   to: 377
    # HitCount: 1
    #
    # Pattern_name Mismatch Pattern
    # pattern1            0 [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
    #
    #=======================================

      Start     End Pattern_name Mismatch Sequence
         55      65 pattern1            . YVGDEAQSKRG

    #---------------------------------------
    #---------------------------------------
    #=======================================
    #
    # Sequence: ACTSB_FUGRU     from: 1   to: 377
    # HitCount: 1
    #
    # Pattern_name Mismatch Pattern
    # pattern1            0 [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
    #
    #=======================================

      Start     End Pattern_name Mismatch Sequence
         55      65 pattern1            . YVGDEAQSKRG

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

    #---------------------------------------
    # Total_sequences: 8
    # Total_hitcount: 8
    #---------------------------------------

## 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 | Reports on protein proteolytic enzyme or reagent cleavage sites
epestfind | Finds PEST motifs as potential proteolytic cleavage sites
fuzztran | Search for patterns in protein sequences (translated)
helixturnhelix | Identify nucleic acid-binding motifs in protein sequences
oddcomp | Identify proteins with specified sequence word composition
patmatdb | Searches protein sequences with a sequence motif
patmatmotifs | Scan a protein sequence with motifs from the PROSITE database
pepcoil | Predicts coiled coil regions in protein sequences
preg | Regular expression search of protein sequence(s)
pscan | Scans protein sequence(s) with fingerprints from the PRINTS database
sigcleave | Reports on signal cleavage sites in a protein sequence

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 (ajb © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, 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