|   | fuzzpro | 
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.
| % 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
| 
   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
 | 
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) | Protein sequence(s) filename and optional format, or reference (input 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 | Property value(s) | |
| [-outfile] (Parameter 2) | Output report file name | Report output file | <*>.fuzzpro | 
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
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'.
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.
| 
########################################
# 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
#---------------------------------------
 | 
| 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: