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EMBOSS: patmatdb |
The motif is converted to a regular expression, and matches are completed using Henry Spencer's regular expression library of functions.
It returns the number of matches there were between the motif and each matched sequence, length of match, start and end positions of match, and writes out an alignment.
% patmatdb Search a protein sequence with a motif Input sequence(s): sw:* Protein motif to search for: st[ty]s Output file [5h1d_fugru.patmatdb]:
Mandatory qualifiers: [-sequence] seqall Sequence database USA [-motif] string Patterns for patmatdb are based on the format of pattern used in the PROSITE database. For example: '[DE](2)HS{P}X(2)PX(2,4)C' 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'. [-outfile] outfile Output file name Optional qualifiers: (none) Advanced qualifiers: (none) |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
[-motif] (Parameter 2) |
Patterns for patmatdb are based on the format of pattern used in the PROSITE database. For example: '[DE](2)HS{P}X(2)PX(2,4)C' 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'. | A string of at least 2 characters | Required |
[-outfile] (Parameter 3) |
Output file name | Output file | <sequence>.patmatdb |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced 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'.
Number of matches found in HD_FUGRU = 1 Length of the sequence = 3148 basepairs Length of match = 4 Start of match = position 1037 of sequence End of match = position 1040 of sequence patmatDB of HD_FUGRU from 1037 to 1040 using pattern st[ty]s STPASSTTSSAVDP | | 1037 1040 Number of matches found in GCN4_YEAST = 1 Length of the sequence = 281 basepairs Length of match = 4 Start of match = position 157 of sequence End of match = position 160 of sequence patmatDB of GCN4_YEAST from 157 to 160 using pattern st[ty]s SNLEVSTTSFLPTP | | 157 160
Program name | Description |
---|---|
dreg | regular expression search of a nucleotide sequence |
fuzznuc | Nucleic acid pattern search |
fuzzpro | Protein pattern search |
fuzztran | Protein pattern search after translation |
helixturnhelix | Report nucleic acid binding motifs |
patmatmotifs | Search a PROSITE motif database with a protein sequence |
preg | regular expression search of a protein sequence |
printsextract | Extract data from PRINTS |
prosextract | Builds the PROSITE motif database for patmatmotifs to search |
pscan | Scans proteins using PRINTS |
tfscan | Scans DNA sequences for transcription factors |