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patmatdb |
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patmatdb searches the input protein sequences for the specified sequence motif. The output is a standard EMBOSS report file including the number of matches between the motif and each input sequence, length of match, start and end positions of match, and the motif-sequence alignment. 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.
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. 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. (Any string of at least 2 characters).
% patmatdb Searches protein sequences with a sequence motif Input protein sequence(s): tsw:* Protein motif to search for: st[ty]s Output report [12s1_arath.patmatdb]: ajSeqxrefNewDbS '1-I' 'FT025' |
Go to the input files for this example
Go to the output files for this example
Searches protein sequences with a sequence motif
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-sequence] seqall Protein sequence(s) filename and optional
format, or reference (input 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'. (Any string of at least 2
characters)
[-outfile] report [*.patmatdb] Output report file name
(default -rformat dbmotif)
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
-rstrandshow3 boolean Show the nucleotide strand in the report
-rusashow3 boolean Show the full USA in the report
-rmaxall3 integer Maximum total hits to report
-rmaxseq3 integer Maximum hits to report for one sequence
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to 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 and exit. 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 dying program messages
-version boolean Report version number and exit
|
| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) |
seqall | Protein sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
| [-motif] (Parameter 2) |
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'. | Any string of at least 2 characters | Required |
| [-outfile] (Parameter 3) |
report | Output report file name | (default -rformat dbmotif) | <*>.patmatdb |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-sequence" associated seqall qualifiers | ||||
| -sbegin1 -sbegin_sequence |
integer | Start of each sequence to be used | Any integer value | 0 |
| -send1 -send_sequence |
integer | End of each sequence to be used | Any integer value | 0 |
| -sreverse1 -sreverse_sequence |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask1 -sask_sequence |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide1 -snucleotide_sequence |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein1 -sprotein_sequence |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower1 -slower_sequence |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper1 -supper_sequence |
boolean | Make upper case | Boolean value Yes/No | N |
| -sformat1 -sformat_sequence |
string | Input sequence format | Any string | |
| -sdbname1 -sdbname_sequence |
string | Database name | Any string | |
| -sid1 -sid_sequence |
string | Entryname | Any string | |
| -ufo1 -ufo_sequence |
string | UFO features | Any string | |
| -fformat1 -fformat_sequence |
string | Features format | Any string | |
| -fopenfile1 -fopenfile_sequence |
string | Features file name | Any string | |
| "-outfile" associated report qualifiers | ||||
| -rformat3 -rformat_outfile |
string | Report format | Any string | dbmotif |
| -rname3 -rname_outfile |
string | Base file name | Any string | |
| -rextension3 -rextension_outfile |
string | File name extension | Any string | |
| -rdirectory3 -rdirectory_outfile |
string | Output directory | Any string | |
| -raccshow3 -raccshow_outfile |
boolean | Show accession number in the report | Boolean value Yes/No | N |
| -rdesshow3 -rdesshow_outfile |
boolean | Show description in the report | Boolean value Yes/No | N |
| -rscoreshow3 -rscoreshow_outfile |
boolean | Show the score in the report | Boolean value Yes/No | Y |
| -rstrandshow3 -rstrandshow_outfile |
boolean | Show the nucleotide strand in the report | Boolean value Yes/No | Y |
| -rusashow3 -rusashow_outfile |
boolean | Show the full USA in the report | Boolean value Yes/No | N |
| -rmaxall3 -rmaxall_outfile |
integer | Maximum total hits to report | Any integer value | 0 |
| -rmaxseq3 -rmaxseq_outfile |
integer | Maximum hits to report for one sequence | Any integer value | 0 |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N |
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
| -warning | boolean | Report warnings | Boolean value Yes/No | Y |
| -error | boolean | Report errors | Boolean value Yes/No | Y |
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y |
| -version | boolean | Report version number and exit | Boolean value Yes/No | N |
The input is a standard EMBOSS sequence query (also known as a 'USA').
Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
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, dasgff, debug, listfile, dbmotif, diffseq, draw, restrict, excel, feattable, motif, nametable, regions, seqtable, simple, srs, table, tagseq.
See: http://emboss.sf.net/docs/themes/ReportFormats.html for further information on report formats.
By default the output is in 'dbmotif' format.
########################################
# Program: patmatdb
# Rundate: Fri 15 Jul 2011 12:00:00
# Commandline: patmatdb
# -sequence "tsw:*"
# -motif "st[ty]s"
# Report_format: dbmotif
# Report_file: 12s1_arath.patmatdb
########################################
#=======================================
#
# 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: HD_TAKRU 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: PAXI_HUMAN from: 1 to: 591
# HitCount: 1
#
# Motif: ST[TY]S
#
#=======================================
Length = 4
Start = position 13 of sequence
End = position 16 of sequence
LADLESTTSHISKR
| |
13 16
#---------------------------------------
#---------------------------------------
#---------------------------------------
# Total_sequences: 100
# Total_length: 35357
# Reported_sequences: 3
# Reported_hitcount: 3
#---------------------------------------
|
| Program name | Description |
|---|---|
| antigenic | Finds antigenic sites in proteins |
| epestfind | Finds PEST motifs as potential proteolytic cleavage sites |
| fuzzpro | Search for patterns in protein sequences |
| fuzztran | Search for patterns in protein sequences (translated) |
| patmatmotifs | Scan a protein sequence with motifs from the PROSITE database |
| preg | Regular expression search of protein sequence(s) |
| pscan | Scans protein sequence(s) with fingerprints from the PRINTS database |
| sigcleave | Reports on signal cleavage sites in a protein sequence |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.