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EMBOSS: 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 Search pattern -mismatch integer Number of mismatches [-outf] outfile Output file name Optional qualifiers: (none) Advanced qualifiers: -mmshow bool Show mismatches -accshow bool Show accession numbers -descshow bool Show descriptions |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
-pattern | Search pattern | Any string is accepted | An empty string is accepted |
-mismatch | Number of mismatches | Integer 0 or more | 0 |
[-outf] (Parameter 2) |
Output file name | Output file | <sequence>.fuzzpro |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-mmshow | Show mismatches | Yes/No | No |
-accshow | Show accession numbers | Yes/No | No |
-descshow | Show descriptions | Yes/No | No |
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'.
ACT1_FUGRU 53 YVGDEAQSKRG ACT2_FUGRU 53 YVGDEAQSKRG ACT3_FUGRU 53 YVGDEAQSKRG ACTC_FUGRU 55 YVGDEAQSKRG ACTS_FUGRU 55 YVGDEAQSKRG ACTT_FUGRU 55 YVGDEAQSKRG
It is composed of three columns of data.
If the option '-mmshow' is used, then an extra column of data is output indicating how many mismatches there are:
% fuzzpro -mmshow Protein pattern search Input sequence(s): sw:100k_rat Search pattern: RARLX(3)R Number of mismatches [0]: 1 Output file [100k_rat.fuzzpro]: stdout 100K_RAT 613 1 EARLNCFRN
Program name | Description |
---|---|
dreg | regular expression search of a nucleotide sequence |
fuzznuc | Nucleic acid pattern search |
fuzztran | Protein pattern search after translation |
patmatdb | Search a protein sequence with a motif |
patmatmotifs | Search a PROSITE motif database with a protein sequence |
preg | regular expression search of a protein sequence |
pscan | Scans proteins using PRINTS |
tfscan | Scans DNA sequences for transcription factors |
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: