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<div class="title">DecoyDatabase </div> </div>
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<div class="textblock"><p>Create a decoy peptide database from standard FASTA databases.</p>
<p>Decoy databases are useful to control false discovery rates and thus estimate score cutoffs for identified spectra.</p>
<p>The decoy can either be generated from reversed or shuffled sequences.</p>
<p>To get a 'contaminants' database have a look at <a href="http://www.thegpm.org/crap/index.html">http://www.thegpm.org/crap/index.html</a> or find/create your own contaminant database.</p>
<p>Multiple databases can be provided as input, which will internally be concatenated before being used for decoy generation. This allows you to specify your target database plus a contaminant file and (upon using the <code>append</code> flag) obtain a concatenated target-decoy database using a single call, e.g., DecoyDatabase -in human.fasta crap.fasta -out human_TD.fasta -append</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
DecoyDatabase -- Create decoy peptide databases from normal ones.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
DecoyDatabase <options>
Options (mandatory options marked with '*'):
-in <file(s)>* Input FASTA file(s), each containing a database. It is recommended to includ
e a contaminant database as well. (valid formats: 'fasta')
-out <file>* Output FASTA file where the decoy database will be written to. (valid format
s: 'fasta')
-decoy_string <string> String that is appended to the accession of the protein database to indicate
a decoy protein. (default: '_rev')
-decoy_string_position <enum> Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the
protein accession? (default: 'suffix' valid: 'prefix', 'suffix')
-append If this flag is used, the decoy database is appended to the target database,
allowing combined target decoy searches.
-shuffle If 'true' then the decoy hit are shuffled from the target sequences, otherwi
se they are reversed
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">+DecoyDatabase</span><span class="node_description">Create decoy peptide databases from normal ones.</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 'DecoyDatabase'</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">Input FASTA file(s), each containing a database. It is recommended to include a contaminant database as well.</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 FASTA file where the decoy database will be written to.</span><span class="item_tags">output file</span><span class="item_restrictions">*.fasta</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">decoy_string</span><span class="item_value">_rev</span>
<span class="item_description">String that is appended to the accession of the protein database to indicate a decoy protein.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">decoy_string_position</span><span class="item_value">suffix</span>
<span class="item_description">Should the 'decoy_string' be prepended (prefix) or appended (suffix) to the protein accession?</span><span class="item_tags"></span><span class="item_restrictions">prefix,suffix</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">append</span><span class="item_value">false</span>
<span class="item_description">If this flag is used, the decoy database is appended to the target database, allowing combined target decoy searches.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">shuffle</span><span class="item_value">false</span>
<span class="item_description">If 'true' then the decoy hit are shuffled from the target sequences, otherwise they are reversed</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;">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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