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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
author rmarenco
date Wed, 13 Jul 2016 13:36:37 -0400
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1 <h1 id="conversion-of-ncbi-blast-tblastn-results-to-psl-format">Conversion of NCBI BLAST+ tblastn results to PSL format</h1>
2 <p>Wilson Leung <script type="text/javascript">
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8 <p>Last Update: 04/24/2016</p>
9 <h2 id="version-information">Version information</h2>
10 <ul>
11 <li>Kent source tree: v324</li>
12 <li>NCBI BLAST+: BLAST 2.2.30+</li>
13 </ul>
14 <h2 id="data-sources">Data sources</h2>
15 <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&amp;id=FBgn0004859&amp;chr=4&amp;dump=PrecompiledFasta&amp;targetset=translation">FlyBase</a>.</p>
16 <ul>
17 <li>Dbia3.fa = contig1 sequence in the Dbia3 asssembly</li>
18 <li>ci.pep = Protein sequences for the three isoforms of the <em>ci</em> gene in <em>D. melanogaster</em></li>
19 </ul>
20 <h2 id="conversion-protocol">Conversion protocol</h2>
21 <ol style="list-style-type: decimal">
22 <li><p>Create BLAST database for the assembly</p>
23 <pre><code>makeblastdb -in Dbia3.fa -dbtype nucl</code></pre></li>
24 <li><p>Perform tblastn search and output results in XML format</p>
25 <pre><code>tblastn -outfmt 5 -db Dbia3.fa -query ci.pep -out tblastn_Dbia3_ci.xml -evalue 1e-2</code></pre></li>
26 <li><p>Convert results into PSL format</p>
27 <pre><code>blastXmlToPsl -convertToNucCoords tblastn_Dbia3_ci.xml tblastn_Dbia3_ci.xml.psl</code></pre></li>
28 <li><p>Convert PSL output into BED format</p>
29 <pre><code>pslToBed tblastn_Dbia3_ci.xml.psl tblastn_Dbia3_ci.xml.bed</code></pre></li>
30 </ol>
31 <h2 id="output-files">Output files</h2>
32 <ul>
33 <li>tblastn_Dbia3_ci.xml = tblastn results in XML format</li>
34 <li>tblastn_Dbia3_ci.xml.psl = tblastn results in PSL format</li>
35 <li>tblastn_Dbia3_ci.xml.bed = tblastn results in BED format</li>
36 </ul>