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
Standard (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 Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outfile" associated qualifiers -rformat3 string Report format -rname3 string Base file name -rextension3 string File name extension -rdirectory3 string Output directory -raccshow3 boolean Show accession number in the report -rdesshow3 boolean Show description in the report -rscoreshow3 boolean Show the score in the report -rusashow3 boolean Show the full USA in the report General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report deaths |
Standard (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 | |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) 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://emboss.sf.net/docs/themes/ReportFormats.html for further information on report formats.
By default patmatdb writes a 'dbmotif' report file.
######################################## # Program: patmatdb # Rundate: Fri Jul 15 2005 12:00:00 # 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 |
epestfind | Finds PEST motifs as potential proteolytic cleavage sites |
fuzzpro | Protein pattern search |
fuzztran | Protein pattern search after translation |
helixturnhelix | Report nucleic acid binding motifs |
oddcomp | Find 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 |