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<HTML>
<HEAD>
<TITLE>
EMBOSS: patmatdb
</TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">
<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
patmatdb
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
Search a protein sequence with a motif
<H2>
Description
</H2>
Takes a protein motif and compares it to a set of protein sequences.
<p>
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.
<H2>
Usage
</H2>
<b>Here is a sample session with patmatdb</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>patmatdb </b>
Search a protein sequence with a motif
Input protein sequence(s): <b>tsw:*</b>
Protein motif to search for: <b>st[ty]s</b>
Output report [edd1_rat.patmatdb]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
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
-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 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 dying program messages
</pre>
</td></tr></table>
<P>
<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Standard (Mandatory) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td>[-sequence]<br>(Parameter 1)</td>
<td>Protein sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>[-motif]<br>(Parameter 2)</td>
<td>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'.</td>
<td>Any string of at least 2 characters</td>
<td><b>Required</b></td>
</tr>
<tr>
<td>[-outfile]<br>(Parameter 3)</td>
<td>Output report file name</td>
<td>Report output file</td>
<td><i><*></i>.patmatdb</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Additional (Optional) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
<tr bgcolor="#FFFFCC">
<th align="left" colspan=2>Advanced (Unprompted) qualifiers</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>
<tr>
<td colspan=4>(none)</td>
</tr>
</table>
<H2>
Input file format
</H2>
<b>patmatdb</b> reads in one or more protein sequence USAs.
<p>
<a name="input.1"></a>
<h3>Input files for usage example </h3>
'tsw:*' is a sequence entry in the example protein database 'tsw'
<p>
<p>
<h3>Pattern specification</h3>
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.
<p>
The PROSITE pattern definition from the PROSITE documentation follows.
<ul>
<li> The standard IUPAC one-letter codes for the amino acids are used.
<li> The symbol `x' is used for a position where any amino acid is
accepted.
<li> 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.
<li> 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.
<li> Each element in a pattern is separated from its neighbor by a
`-'. (Optional in patmatdb).
<li> 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.
<li> 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.
<li> A period ends the pattern. (Optional in patmatdb).
</ul>
<p>
For example, in SWISSPROT entry 100K_RAT you can look for the pattern:
<p>
<pre>
[DE](2)HS{P}X(2)PX(2,4)C
</pre>
<p>
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.
<p>
The search is case-independent, so 'AAA' matches 'aaa'.
<H2>
Output file format
</H2>
<p>
The output is a standard EMBOSS report file.
<p>
The results can be output in one of several styles by using the
command-line qualifier <b>-rformat xxx</b>, 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
<p>
See:
<A href="http://emboss.sf.net/docs/themes/ReportFormats.html">
http://emboss.sf.net/docs/themes/ReportFormats.html</A>
for further information on report formats.
<p>
<p>
By default <b>patmatdb</b> writes a 'dbmotif' report file.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: edd1_rat.patmatdb </h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
########################################
# Program: patmatdb
# Rundate: Sun 15 Jul 2007 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
#---------------------------------------
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
None.
<H2>
Notes
</H2>
None.
<H2>
References
</H2>
<ol>
<li>Bairoch, A., Bucher P. (1994) PROSITE: recent developments. Nucleic
Acids Research, Vol 22, No.17 3583-3589.
<li>Bairoch, A., (1992) PROSITE: a dictionary of sites and patterns in
proteins. Nucleic Acids Research, Vol 20, Supplement, 2013-2018.
<li>Peek, J., O'Reilly, T., Loukides, M., (1997) Unix Power Tools, 2nd
Edition.
<li>Gusfield, D., (1997) Algorithms on strings, Trees and Sequences.
<li>Sedgewick, R,. (1990) Algorithms in C.
</ol>
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
None.
<H2>
Exit status
</H2>
It always exits with status 0
<H2>
Known bugs
</H2>
None.
<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th><th>Description</th></tr>
<tr>
<td><a href="antigenic.html">antigenic</a></td>
<td>Finds antigenic sites in proteins</td>
</tr>
<tr>
<td><a href="digest.html">digest</a></td>
<td>Protein proteolytic enzyme or reagent cleavage digest</td>
</tr>
<tr>
<td><a href="epestfind.html">epestfind</a></td>
<td>Finds PEST motifs as potential proteolytic cleavage sites</td>
</tr>
<tr>
<td><a href="fuzzpro.html">fuzzpro</a></td>
<td>Protein pattern search</td>
</tr>
<tr>
<td><a href="fuzztran.html">fuzztran</a></td>
<td>Protein pattern search after translation</td>
</tr>
<tr>
<td><a href="helixturnhelix.html">helixturnhelix</a></td>
<td>Report nucleic acid binding motifs</td>
</tr>
<tr>
<td><a href="oddcomp.html">oddcomp</a></td>
<td>Find protein sequence regions with a biased composition</td>
</tr>
<tr>
<td><a href="patmatmotifs.html">patmatmotifs</a></td>
<td>Search a PROSITE motif database with a protein sequence</td>
</tr>
<tr>
<td><a href="pepcoil.html">pepcoil</a></td>
<td>Predicts coiled coil regions</td>
</tr>
<tr>
<td><a href="preg.html">preg</a></td>
<td>Regular expression search of a protein sequence</td>
</tr>
<tr>
<td><a href="pscan.html">pscan</a></td>
<td>Scans proteins using PRINTS</td>
</tr>
<tr>
<td><a href="sigcleave.html">sigcleave</a></td>
<td>Reports protein signal cleavage sites</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Sinead O'Leary (current e-mail address unknown)
<br>
while she was at:
<br>
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK
<H2>
History
</H2>
Completed April 30 1999.
<H2>
Target users
</H2>
This program is intended to be used by everyone and everything, from naive users to embedded scripts.
<H2>
Comments
</H2>
None
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</HTML>
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