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     Output report file name

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                boolean    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)
Output report file name 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.

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 nameDescription
antigenicFinds antigenic sites in proteins
digestProtein proteolytic enzyme or reagent cleavage digest
fuzztranProtein pattern search after translation
helixturnhelixReport nucleic acid binding motifs
oddcompFinds protein sequence regions with a biased composition
patmatdbSearch a protein sequence with a motif
patmatmotifsSearch a PROSITE motif database with a protein sequence
pepcoilPredicts coiled coil regions
pregRegular expression search of a protein sequence
pscanScans proteins using PRINTS
sigcleaveReports 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:

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