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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
author | rmarenco |
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date | Wed, 13 Jul 2016 13:36:37 -0400 |
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<h1 id="conversion-of-ncbi-blast-tblastn-results-to-psl-format">Conversion of NCBI BLAST+ tblastn results to PSL format</h1> <p>Wilson Leung <script type="text/javascript"> <!-- h='wustl.edu';a='@';n='wleung';e=n+a+h; document.write('<a h'+'ref'+'="ma'+'ilto'+':'+e+'" clas'+'s="em' + 'ail">'+e+'<\/'+'a'+'>'); // --> </script><noscript>wleung at wustl dot edu</noscript></p> <p>Last Update: 04/24/2016</p> <h2 id="version-information">Version information</h2> <ul> <li>Kent source tree: v324</li> <li>NCBI BLAST+: BLAST 2.2.30+</li> </ul> <h2 id="data-sources">Data sources</h2> <p>For testing purposes, the database consists of only contig1 in the Dbia3 assembly while the protein sequences correspond to the three isoforms of the <em>D. melanogaster</em> <em>ci</em> gene in contig1. The protein sequences are available through <a href="http://flybase.org/cgi-bin/getseq.html?source=dmel&id=FBgn0004859&chr=4&dump=PrecompiledFasta&targetset=translation">FlyBase</a>.</p> <ul> <li>Dbia3.fa = contig1 sequence in the Dbia3 asssembly</li> <li>ci.pep = Protein sequences for the three isoforms of the <em>ci</em> gene in <em>D. melanogaster</em></li> </ul> <h2 id="conversion-protocol">Conversion protocol</h2> <ol style="list-style-type: decimal"> <li><p>Create BLAST database for the assembly</p> <pre><code>makeblastdb -in Dbia3.fa -dbtype nucl</code></pre></li> <li><p>Perform tblastn search and output results in XML format</p> <pre><code>tblastn -outfmt 5 -db Dbia3.fa -query ci.pep -out tblastn_Dbia3_ci.xml -evalue 1e-2</code></pre></li> <li><p>Convert results into PSL format</p> <pre><code>blastXmlToPsl -convertToNucCoords tblastn_Dbia3_ci.xml tblastn_Dbia3_ci.xml.psl</code></pre></li> <li><p>Convert PSL output into BED format</p> <pre><code>pslToBed tblastn_Dbia3_ci.xml.psl tblastn_Dbia3_ci.xml.bed</code></pre></li> </ol> <h2 id="output-files">Output files</h2> <ul> <li>tblastn_Dbia3_ci.xml = tblastn results in XML format</li> <li>tblastn_Dbia3_ci.xml.psl = tblastn results in PSL format</li> <li>tblastn_Dbia3_ci.xml.bed = tblastn results in BED format</li> </ul>