EMBOSS: fuzzpro manual

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: Fri Jul 15 2005 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.

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

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

Function

Description

Usage

Command line arguments

Input file format

Input files for usage example

Pattern specification

Output file format

Output files for usage example

File: 100k_rat.fuzzpro

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments