
                                 patmatdb 



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 [edd1_rat.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

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.
     * The standard IUPAC one-letter codes for the amino acids are used.
     * The symbol `x' is used for a position where any amino acid is
       accepted.
     * Ambiguities are indicated by listing the acceptable amino acids
       for a given position, between square parentheses `[ ]'. For
       example: [ALT] stands for Ala or Leu or Thr.
     * Ambiguities are also indicated by listing between a pair of curly
       brackets `{ }' the amino acids that are not accepted at a given
       position. For example: {AM} stands for any amino acid except Ala
       and Met.
     * Each element in a pattern is separated from its neighbor by a `-'.
       (Optional in patmatdb).
     * Repetition of an element of the pattern can be indicated by
       following that element with a numerical value or a numerical range
       between parenthesis. Examples: x(3) corresponds to x-x-x, x(2,4)
       corresponds to x-x or x-x-x or x-x-x-x.
     * When a pattern is restricted to either the N- or C-terminal of a
       sequence, that pattern either starts with a `<' symbol or
       respectively ends with a `>' symbol.
     * A period ends the pattern. (Optional in patmatdb).

   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: edd1_rat.patmatdb

########################################
# Program: patmatdb
# Rundate: Tue 15 Jul 2008 12:00:00
# Commandline: patmatdb
#    -sequence "tsw:*"
#    -motif "st[ty]s"
# Report_format: dbmotif
# Report_file: edd1_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: 591
# HitCount: 1
#
# Motif: ST[TY]S
#
#=======================================

Length = 4
Start = position 13 of sequence
End = position 16 of sequence


LADLESTTSHISKR
     |  |
    13  16


#---------------------------------------
#---------------------------------------

#---------------------------------------
# Total_sequences: 3
# Total_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
