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HTML>
fuzzpro
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
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 [cru4_arath.fuzzpro]:
Go to the input files for this example
Go to the output files for this example
Command line arguments
Search for patterns in protein sequences
Version: EMBOSS:6.6.0.0
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 (default
-rformat seqtable)
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
-scircular1 boolean Sequence is circular
-squick1 boolean Read id and sequence only
-sformat1 string Input sequence format
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-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 and exit. 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
-version boolean Report version number and exit
Input file format
fuzzpro reads in one or more protein sequences.
The input is a standard EMBOSS sequence query (also known as a 'USA').
Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier
-sformat xxx, where 'xxx' is replaced by the name of the required
format. The available format names are: gff (gff3), gff2, embl (em),
genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
dasgff and debug.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
information on sequence formats.
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 neighbour 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, dasgff, debug, listfile, dbmotif, diffseq,
draw, restrict, excel, feattable, motif, nametable, 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: cru4_arath.fuzzpro
########################################
# Program: fuzzpro
# Rundate: Mon 15 Jul 2013 12:00:00
# Commandline: fuzzpro
# -sequence "tsw:*"
# -pattern "[FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G"
# Report_format: seqtable
# Report_file: cru4_arath.fuzzpro
########################################
#=======================================
#
# Sequence: ACTB1_TAKRU from: 1 to: 375
# HitCount: 1
#
# Pattern_name Mismatch Pattern
# pattern 0 [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
#
#=======================================
Start End Pattern Mismatch Sequence
53 63 pattern:[FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G . YVGDEAQSKR
G
#---------------------------------------
#---------------------------------------
#=======================================
#
# Sequence: ACTB2_TAKRU from: 1 to: 375
# HitCount: 1
#
# Pattern_name Mismatch Pattern
# pattern 0 [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
#
#=======================================
Start End Pattern Mismatch Sequence
53 63 pattern:[FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G . YVGDEAQSKR
G
#---------------------------------------
#---------------------------------------
#=======================================
#
# Sequence: ACTB3_TAKRU from: 1 to: 375
# HitCount: 1
#
# Pattern_name Mismatch Pattern
# pattern 0 [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
#
#=======================================
[Part of this file has been deleted for brevity]
#
# Sequence: ACTSA_TAKRU from: 1 to: 377
# HitCount: 1
#
# Pattern_name Mismatch Pattern
# pattern 0 [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
#
#=======================================
Start End Pattern Mismatch Sequence
55 65 pattern:[FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G . YVGDEAQSKR
G
#---------------------------------------
#---------------------------------------
#=======================================
#
# Sequence: ACTSB_TAKRU from: 1 to: 377
# HitCount: 1
#
# Pattern_name Mismatch Pattern
# pattern 0 [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
#
#=======================================
Start End Pattern Mismatch Sequence
55 65 pattern:[FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G . YVGDEAQSKR
G
#---------------------------------------
#---------------------------------------
#=======================================
#
# Sequence: ACTS_OREMO from: 1 to: 377
# HitCount: 1
#
# Pattern_name Mismatch Pattern
# pattern 0 [FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G
#
#=======================================
Start End Pattern Mismatch Sequence
55 65 pattern:[FY]-[LIV]-G-[DE]-E-A-Q-x-[RKQ](2)-G . YVGDEAQSKR
G
#---------------------------------------
#---------------------------------------
#---------------------------------------
# Total_sequences: 100
# Total_length: 37225
# Reported_sequences: 8
# Reported_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 Find antigenic sites in proteins
epestfind Find PEST motifs as potential proteolytic cleavage sites
fuzztran Search for patterns in protein sequences (translated)
patmatdb Search protein sequences with a sequence motif
patmatmotifs Scan a protein sequence with motifs from the PROSITE
database
preg Regular expression search of protein sequence(s)
pscan Scan protein sequence(s) with fingerprints from the PRINTS
database
sigcleave Report on signal cleavage sites in a protein sequence
Author(s)
Alan Bleasby
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
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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