
                              EMBOSS: patmatdb
     _________________________________________________________________
   
                               Program patmatdb
                                       
Function

   Search a protein sequence with a motif
   
Description

   Takes a protein motif and compares it to a set of protein sequences.
   
   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.
   
Usage

   Here is a sample session with patmatdb.
   
% patmatdb
Search a protein sequence with a motif
Input sequence(s): sw:*
Protein motif to search for: st[ty]s
Output file [5h1d_fugru.patmatdb]:

Command line arguments

   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     (no help text) report value

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       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) (no help text) report value Report file
   Optional qualifiers Allowed values Default
   (none)
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

   It reads in one or more protein sequences.
   
   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://www.uk.embnet.org/Software/EMBOSS/Themes/ReportFormats.html for
   further information on report formats.
   
   By default patmatdb writes a 'dbmotif' report file.
   
   The output from the above example follows:
     _________________________________________________________________
   
########################################
# Program: patmatdb
# Rundate: Thu Apr 11 13:56:31 2002
# Report_file: 5h1d_fugru.patmatdb
########################################

#=======================================
#
# Sequence: 2AAA_YEAST     from: 1   to: 635
# HitCount: 2
#
# Motif: ST[TY]S
#
#=======================================

Length = 4
Start = position 19 of sequence
End = position 22 of sequence


SAATTSTTSTTSNS
     |  |
    19  22

Length = 4
Start = position 22 of sequence
End = position 25 of sequence


TTSTTSTTSNSKDS
     |  |
    22  25


#---------------------------------------
#---------------------------------------
#=======================================
#
# Sequence: 41_XENLA     from: 1   to: 801
# HitCount: 1
#
# Motif: ST[TY]S
#
#=======================================

Length = 4
Start = position 52 of sequence
End = position 55 of sequence


SQESPSTTSPSTRK
     |  |
    52  55

etc.
     _________________________________________________________________
   
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         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
   preg           Regular expression search of a protein sequence
   pscan          Scans proteins using PRINTS
   sigcleave      Reports protein signal cleavage sites
   
   fuzzpro - Protein pattern search
   This does much the same is patmatdb, but has a slightly different
   style of output and allows mismatches.
   
   patmatmotifs - Compares a protein sequence to the PROSITE motif
   database.
   This does the opposite to patmatdb, comparing a database of motifs to
   one sequence.
   
Author(s)

   This application was written by Sinead O'Leary
   (soleary@hgmp.mrc.ac.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
