
                                  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 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
   -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 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 dying program messages

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: Sun 15 Jul 2007 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         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        Find 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 (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
