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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 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]:
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) |
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'.
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.
Program name | Description |
---|---|
antigenic | Finds antigenic sites in proteins |
digest | Protein proteolytic enzyme or reagent cleavage digest |
fuzztran | Protein pattern search after translation |
helixturnhelix | Report nucleic acid binding motifs |
oddcomp | Finds 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: