http://stab.st-andrews.ac.uk/wiki/index.php?action=history&feed=atom&title=BlatBlat - Revision history2026-05-10T02:54:52ZRevision history for this page on the wikiMediaWiki 1.30.0http://stab.st-andrews.ac.uk/wiki/index.php?title=Blat&diff=1747&oldid=prevRf at 15:53, 5 June 20172017-06-05T15:53:07Z<p></p>
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<td colspan="2" style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: white; color:black; text-align: center;">Revision as of 15:53, 5 June 2017</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l4" >Line 4:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>= Usage =</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>= Usage =</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"> module load blat</ins></div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">to load up the module.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Typical usage would be to, given a reference sequence for a gene, to look for that gene sequence in a different reference.  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Typical usage would be to, given a reference sequence for a gene, to look for that gene sequence in a different reference.  </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* the database FASTA does not need indexing, and it comes first in the list of arguments. Databse often abbreviated to '''T''' for target.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* the database FASTA does not need indexing, and it comes first in the list of arguments. Databse often abbreviated to '''T''' for target.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* the query is second, query often abbreviated to '''Q'''.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* the query is second, query often abbreviated to '''Q'''.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* the ouput file is in its own format, <del class="diffchange diffchange-inline">caleld </del>PSL, but is easily read in a text editor.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* the ouput file is in its own format, <ins class="diffchange diffchange-inline">called </ins>PSL, but is easily read in a text editor.</div></td></tr>
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</table>Rfhttp://stab.st-andrews.ac.uk/wiki/index.php?title=Blat&diff=1746&oldid=prevRf: Created page with "= Introduction = BLAT is a tool from Jim Kent's stable at UCSD. In purpose it is very close to NCBI's BLAST, but it generally is easier in terms of switches and input options..."2017-06-05T15:52:35Z<p>Created page with "= Introduction = BLAT is a tool from Jim Kent's stable at UCSD. In purpose it is very close to NCBI's BLAST, but it generally is easier in terms of switches and input options..."</p>
<p><b>New page</b></p><div>= Introduction =<br />
<br />
BLAT is a tool from Jim Kent's stable at UCSD. In purpose it is very close to NCBI's BLAST, but it generally is easier in terms of switches and input options.<br />
<br />
= Usage =<br />
<br />
Typical usage would be to, given a reference sequence for a gene, to look for that gene sequence in a different reference. <br />
<br />
blat <db.fa> <query> out.psl<br />
<br />
<ins>Explanation</ins>:<br />
* There are no mandatory switches (there are optional ones though, for example --ooc for an external 11-mer file)<br />
* the database FASTA does not need indexing, and it comes first in the list of arguments. Databse often abbreviated to '''T''' for target.<br />
* the query is second, query often abbreviated to '''Q'''.<br />
* the ouput file is in its own format, caleld PSL, but is easily read in a text editor.</div>Rf