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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
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