patmatdb

 

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Function

Searches protein sequences with a sequence motif

Description

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.

Algorithm

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).

Usage

Here is a sample session with patmatdb


% 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]: 

Go to the input files for this example
Go to the output files for this example

Command line arguments

   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

   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. 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

Standard (Mandatory) qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Protein sequence(s) filename and optional format, or reference (input 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'. Any string of at least 2 characters Required
[-outfile]
(Parameter 3)
Output report file name Report output file <*>.patmatdb
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
(none)

Input file format

patmatdb reads in one or more protein sequence USAs.

Input files for usage example

'tsw:*' is a sequence entry in the example protein database 'tsw'

Pattern specification

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'.

Output file format

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.

Output files for usage example

File: 12s1_arath.patmatdb

########################################
# Program: patmatdb
# Rundate: Tue 15 Jul 2008 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_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: 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: 35263
# Reported_sequences: 3
# Reported_hitcount: 3
#---------------------------------------

Data files

None.

Notes

None.

References

  1. Bairoch, A., Bucher P. (1994) PROSITE: recent developments. Nucleic Acids Research, Vol 22, No.17 3583-3589.
  2. Bairoch, A., (1992) PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Research, Vol 20, Supplement, 2013-2018.
  3. Peek, J., O'Reilly, T., Loukides, M., (1997) Unix Power Tools, 2nd Edition.
  4. Gusfield, D., (1997) Algorithms on strings, Trees and Sequences.
  5. Sedgewick, R,. (1990) Algorithms in C.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0

Known bugs

None.

See also

Program name Description
antigenic Finds antigenic sites in proteins
digest Reports on protein proteolytic enzyme or reagent cleavage sites
epestfind Finds PEST motifs as potential proteolytic cleavage sites
fuzzpro Search for patterns in protein sequences
fuzztran Search for patterns in protein sequences (translated)
helixturnhelix Identify nucleic acid-binding motifs in protein sequences
oddcomp Identify proteins with specified sequence word composition
patmatmotifs Scan a protein sequence with motifs from the PROSITE database
pepcoil Predicts coiled coil regions in protein sequences
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

Author(s)

Sinead O'Leary (current e-mail address unknown)
while she was at:
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

History

Completed April 30 1999.

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None