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EMBOSS: patmatdb |
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] report (no help text) report value Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help bool 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 |
[-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) |
(no help text) report value | Report file | |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
(none) |
Patterns for patmatdb 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 patmatdb writes a 'dbmotif' report file.
The output from the above example follows:
######################################## # Program: patmatdb # Rundate: Thu Apr 11 13:56:31 2002 # Report_file: 5h1d_fugru.patmatdb ######################################## #======================================= # # Sequence: 2AAA_YEAST from: 1 to: 635 # HitCount: 2 # # Motif: ST[TY]S # #======================================= Length = 4 Start = position 19 of sequence End = position 22 of sequence SAATTSTTSTTSNS | | 19 22 Length = 4 Start = position 22 of sequence End = position 25 of sequence TTSTTSTTSNSKDS | | 22 25 #--------------------------------------- #--------------------------------------- #======================================= # # Sequence: 41_XENLA from: 1 to: 801 # HitCount: 1 # # Motif: ST[TY]S # #======================================= Length = 4 Start = position 52 of sequence End = position 55 of sequence SQESPSTTSPSTRK | | 52 55 etc.
Program name | Description |
---|---|
antigenic | Finds antigenic sites in proteins |
digest | Protein proteolytic enzyme or reagent cleavage digest |
fuzzpro | Protein pattern search |
fuzztran | Protein pattern search after translation |
helixturnhelix | Report nucleic acid binding motifs |
oddcomp | Finds protein sequence regions with a biased composition |
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 |
patmatmotifs - Compares a protein
sequence to the PROSITE motif database.
This does the opposite to patmatdb, comparing a database of motifs to
one sequence.