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comparison test-data/tblastN/readme/README.html @ 0:f493979f1408 draft default tip
planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
author | yating-l |
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date | Wed, 21 Dec 2016 12:13:04 -0500 |
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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"> | |
3 <!-- | |
4 h='wustl.edu';a='@';n='wleung';e=n+a+h; | |
5 document.write('<a h'+'ref'+'="ma'+'ilto'+':'+e+'" clas'+'s="em' + 'ail">'+e+'<\/'+'a'+'>'); | |
6 // --> | |
7 </script><noscript>wleung at wustl dot edu</noscript></p> | |
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&id=FBgn0004859&chr=4&dump=PrecompiledFasta&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> |