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<div class="title">DigestorMotif </div> </div>
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<div class="textblock"><p>This application is used to digest a protein database to get all peptides given a cleavage enzyme. It will also produce peptide statistics given the mass accuracy of the instrument. You can extract peptides with specific motifs,e.g. onyl cysteine containing peptides for ICAT experiments. At the moment only trypsin is supported.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
DigestorMotif -- digests a protein database in-silico
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
DigestorMotif <options>
Options (mandatory options marked with '*'):
-in <file>* FASTA input file (valid formats: 'fasta')
-out <file>* Output file (peptides)
(valid formats: 'idXML')
-missed_cleavages <number> The number of allowed missed cleavages (default: '1' min: '0')
-mass_accuracy <number> Give your mass accuracy in ppb (default: '1000')
-min_length <number> Minimum length of peptide (default: '6')
-out_option <number> Indicate 1 (peptide table only), 2 (statistics only) or (both peptide table +
statistics) (default: '1')
-enzyme <string> The digestion enzyme (default: 'Trypsin')
-motif <string> The motif for the restricted peptidome (default: 'M')
Common UTIL options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
</pre><p> <b>INI file documentation of this tool:</b> <div class="ini_global">
<div class="legend">
<b>Legend:</b><br>
<div class="item item_required">required parameter</div>
<div class="item item_advanced">advanced parameter</div>
</div>
<div class="node"><span class="node_name">+DigestorMotif</span><span class="node_description">digests a protein database in-silico</span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:16px;">version</span><span class="item_value">1.11.1</span>
<span class="item_description">Version of the tool that generated this parameters file.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">++1</span><span class="node_description">Instance '1' section for 'DigestorMotif'</span></div>
<div class="item"><span class="item_name item_required" style="padding-left:24px;">in</span><span class="item_value"></span>
<span class="item_description">FASTA input file</span><span class="item_tags">input file</span><span class="item_restrictions">*.fasta</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">output file (peptides)<br></span><span class="item_tags">output file</span><span class="item_restrictions">*.idXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">missed_cleavages</span><span class="item_value">1</span>
<span class="item_description">the number of allowed missed cleavages</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">mass_accuracy</span><span class="item_value">1000</span>
<span class="item_description">give your mass accuracy in ppb</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">min_length</span><span class="item_value">6</span>
<span class="item_description">minimum length of peptide</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">out_option</span><span class="item_value">1</span>
<span class="item_description">indicate 1 (peptide table only), 2 (statistics only) or (both peptide table + statistics)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">enzyme</span><span class="item_value">Trypsin</span>
<span class="item_description">the digestion enzyme</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">motif</span><span class="item_value">M</span>
<span class="item_description">the motif for the restricted peptidome</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">log</span><span class="item_value"></span>
<span class="item_description">Name of log file (created only when specified)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">debug</span><span class="item_value">0</span>
<span class="item_description">Sets the debug level</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">threads</span><span class="item_value">1</span>
<span class="item_description">Sets the number of threads allowed to be used by the TOPP tool</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">no_progress</span><span class="item_value">false</span>
<span class="item_description">Disables progress logging to command line</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">test</span><span class="item_value">false</span>
<span class="item_description">Enables the test mode (needed for internal use only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5</font></TD>
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