/var/lib/mobyle/programs/sig.xml

<?xml version='1.0' encoding='UTF-8'?>
<!-- XML Authors: Corinne Maufrais, Nicolas Joly and Bertrand Neron,             -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris.         -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
  <head>
    <name>sig</name>
    <version>1.0</version>
    <doc>
      <title>sig</title>
      <description>
        <text lang="en">Multiple Prosite motifs searching</text>
      </description>
      <authors>Eric Deveaud</authors>
      <comment>
        <text lang="en">sig  is a program to search  multiple occurences of
	multiple motifs in a set of sequences.</text>
      </comment>
      <sourcelink>ftp://ftp.pasteur.fr/pub/gensoft/projects/sig/</sourcelink>
    </doc>
    <category>sequence:nucleic:pattern</category>
    <category>sequence:protein:pattern</category>
    <command>sig</command>
  </head>
  <parameters>
    <parameter ismandatory="1" issimple="1">
      <name>seqfile</name>
      <prompt lang="en">Protein Sequences</prompt>
      <type>
        <datatype>
          <class>Sequence</class>
        </datatype>
        <dataFormat>FASTA</dataFormat>
      </type>
      <format>
        <code proglang="perl">" $value"</code>
        <code proglang="python">" "+str(value)</code>
      </format>
      <argpos>100</argpos>
    </parameter>
    <parameter ismandatory="1" issimple="1">
      <name>patterns</name>
      <prompt lang="en">Pattern File (-f)</prompt>
      <type>
        <datatype>
          <class>SigPattern</class>
          <superclass>AbstractText</superclass>
        </datatype>
      </type>
      <format>
        <code proglang="perl">(defined $value) ? " -f $value" : ""</code>
        <code proglang="python">("", " -f "+str(value))[value is not None]</code>
      </format>
      <argpos>2</argpos>
      <comment>
        <div xmlns="http://www.w3.org/1999/xhtml">
File format : 
<ul>
<li>one pattern per line.</li> 
<li>A pattern consists in motifs definition separated by distance constraints.</li>
<li>The format is strictly the following: motif_1 (min,max) motif_2 ... (min,max) motif_n, and so on.</li>  
</ul> 
The sig motif syntax follow the syntax used in the PROSITE database :
<h3>Pattern syntax</h3>
  <ol>
    <li>The standard IUPAC one-letter codes for the amino acids are used in PROSITE.</li>
    <li>The symbol `x' is used for a position where any amino acid is accepted.</li>
    <li>Ambiguities are indicated by listing the acceptable amino acids for a 
    given position, between square brackets `[ ]'. For example: [ALT] 
    stands for Ala or Leu or Thr.</li>
    <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>
    <li>Each element in a pattern is separated from its neighbor by a `-'.</li>
    <li>Repetition of an element of the pattern can be indicated by following 
    that element with a numerical value or, if it is a gap ('x'),
     by a numerical range between parentheses.<br/>
      <dl>
        <dt>Examples:</dt>
        <dd>x(3) corresponds to x-x-x</dd>
        <dd>x(2,4) corresponds to x-x or x-x-x or x-x-x-x</dd>
        <dd>A(3) corresponds to A-A-A</dd>
        <dt>Note: You can only use a range with 'x', i.e. A(2,4) is not a valid pattern element.</dt>
      </dl>
   </li>
   <li>When a pattern is restricted to either the N- or C-terminal of a sequence, 
   that pattern either starts with a `&lt;' symbol or respectively ends with a `&gt;' symbol. 
   In some rare cases (<em>e.g.</em> PS00267 or PS00539), '&gt;' can also occur inside square brackets for the C-terminal element. 
'F-[GSTV]-P-R-L-[G&gt;]' means that either 'F-[GSTV]-P-R-L-G' or 'F-[GSTV]-P-R-L&gt;' are considered.</li>
</ol>

the sig pattern ( motifs with distance constraints).
<ul>
<li><strong>[RK]-x-V-x-[FW] (0,) F-x-x-[RK]-x-[RK]</strong>:
    no distance constraints are set between motif [RK]-X-V-X-[FW] and motif F-X-X-[RK]-X-[RK]</li>
<li><strong>[RK]-x-V-x-[FW] (5,15) F-X-X-[RK]-X-[RK]</strong>:
            motif [RK]-X-V-X-[FW] and motif F-X-X-[RK]-X-[RK] should be separated by a gap
            whose length is longer or equal to 5 and shorter or equal to 15.</li>
</ul>            
</div>
      </comment>
      <example>
[RK]-x-V-x-[FW] (0,) F-x-x-[RK]-x-[RK]
[RK]-x-V-x-[FW] (5,15) F-X-X-[RK]-X-[RK]
      </example>
    </parameter>
    <parameter>
      <name>overlapping</name>
      <prompt lang="en">Allows motifs from pattern to be overlapping (-i)</prompt>
      <type>
        <datatype>
          <class>Boolean</class>
        </datatype>
      </type>
      <vdef>
        <value>0</value>
      </vdef>
      <format>
        <code proglang="perl">($value) ? " -i" : ""</code>
        <code proglang="python">("", " -i")[ value ]</code>
      </format>
      <argpos>2</argpos>
    </parameter>
    <parameter>
      <name>reverse</name>
      <prompt lang="en">Searches motifs in ordered and reverse search order, conserving the distance constraints (-r)</prompt>
      <type>
        <datatype>
          <class>Boolean</class>
        </datatype>
      </type>
      <vdef>
        <value>0</value>
      </vdef>
      <format>
        <code proglang="perl">($value) ? " -r" : ""</code>
        <code proglang="python">("", " -r")[ value ]</code>
      </format>
      <argpos>2</argpos>
    </parameter>
  </parameters>
</program>
mobyle-programs 5.1.2-2 / var / lib / mobyle / programs / sig.xml
