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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): tsw:* Protein motif to search for: st[ty]s Output report [100k_rat.patmatdb]: |
Go to the input files for this example
Go to the output files for this example
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 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 |
[-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 report file name | Report output file | |
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'.
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.
######################################## # Program: patmatdb # Rundate: Thu Nov 07 14:35:27 2002 # Report_format: dbmotif # Report_file: 100k_rat.patmatdb ######################################## #======================================= # # Sequence: HD_FUGRU from: 1 to: 3148 # HitCount: 1 # # Motif: ST[TY]S # #======================================= Length = 4 Start = position 1038 of sequence End = position 1041 of sequence STPASSTTSSAVDP | | 1038 1041 #--------------------------------------- #--------------------------------------- #======================================= # # Sequence: GCN4_YEAST from: 1 to: 281 # HitCount: 1 # # Motif: ST[TY]S # #======================================= Length = 4 Start = position 158 of sequence End = position 161 of sequence SNLEVSTTSFLPTP | | 158 161 #--------------------------------------- #--------------------------------------- #======================================= # # Sequence: PAXI_HUMAN from: 1 to: 557 # HitCount: 1 # # Motif: ST[TY]S # #======================================= Length = 4 Start = position 13 of sequence End = position 16 of sequence LADLESTTSHISKR | | 13 16 #--------------------------------------- #--------------------------------------- |
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 |
pestfind | Finds PEST motifs as potential proteolytic cleavage sites |
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.