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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/22770?offset=40</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/37198/understanding-blastn-output-format-6</guid>
	<pubDate>Wed, 27 Jun 2018 18:38:21 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/37198/understanding-blastn-output-format-6</link>
	<title><![CDATA[Understanding BLASTn output format 6 !]]></title>
	<description><![CDATA[<h3 id="sites-page-title-header" style="text-align: left;"><span>BLASTn output format 6</span></h3><div id="sites-canvas-main"><div id="sites-canvas-main-content"><div dir="ltr"><div><div><em>BLASTn</em> maps DNA against DNA, for example gene sequences against a reference genome<br /><br /><code><strong>blastn</strong>  -query <span>genes.ffn</span>  -subject <span>genome.fna</span>  -outfmt <strong>6</strong></code></div><h2>BLASTn tabular output format 6</h2>
<p><strong>Column headers:</strong><br /><code>qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore</code><br /></p>
<table border="1" cellspacing="0">
<tbody>
<tr>
<td> 1.</td>
<td> qseqid</td>
<td> query (e.g., gene) sequence id</td>
</tr>
<tr>
<td> 2.</td>
<td> sseqid</td>
<td> subject (e.g., reference genome) sequence id</td>
</tr>
<tr>
<td> 3.</td>
<td> pident</td>
<td> percentage of identical matches</td>
</tr>
<tr>
<td> 4.</td>
<td> length</td>
<td> alignment length</td>
</tr>
<tr>
<td> 5.</td>
<td> mismatch</td>
<td> number of mismatches</td>
</tr>
<tr>
<td> 6.</td>
<td> gapopen</td>
<td> number of gap openings</td>
</tr>
<tr>
<td> 7.</td>
<td> qstart</td>
<td> start of alignment in query</td>
</tr>
<tr>
<td> 8.</td>
<td> qend</td>
<td> end of alignment in query</td>
</tr>
<tr>
<td> 9.</td>
<td> sstart</td>
<td> start of alignment in subject</td>
</tr>
<tr>
<td> 10.</td>
<td> send</td>
<td> end of alignment in subject</td>
</tr>
<tr>
<td> 11.</td>
<td> evalue</td>
<td> <a href="http://www.metagenomics.wiki/tools/blast/evalue">expect value</a></td>
</tr>
<tr>
<td> 12.</td>
<td> bitscore</td>
<td> <a href="http://www.metagenomics.wiki/tools/blast/evalue"><strong>bit score</strong></a></td>
</tr>
</tbody>
</table>
<p><strong><br /></strong></p>
</div><h2><a name="TOC-Define-your-own-output-format" id="TOC-Define-your-own-output-format"></a>Define your own output format</h2><div><em>by adding the option -outfmt, as for example: </em><strong><br /></strong></div>
<p><code><strong>-outfmt</strong> <strong>"6</strong> <span>qseqid sseqid pident qlen length mismatch gapope evalue bitscore</span><strong>"</strong></code><br /><br /><em><strong>supported format specifiers are:</strong></em><br /><code>qseqid    </code>Query Seq-id<br /><code>qgi       </code>Query GI<br /><code>qacc      </code>Query accesion<br /><code>qaccver   </code>Query accesion.version<br /><code>qlen      </code>Query sequence length<br /><code>sseqid    </code>Subject Seq-id<br /><code>sallseqid </code>All subject Seq-id(s), separated by a ';'<br /><code>sgi       </code>Subject GI<br /><code>sallgi    </code>All subject GIs<br /><code>sacc      </code>Subject accession<br /><code>saccver   </code>Subject accession.version<br /><code>sallacc   </code>All subject accessions<br /><code>slen      </code>Subject sequence length<br /><code>qstart    </code>Start of alignment in query<br /><code>qend      </code>End of alignment in query<br /><code>sstart    </code>Start of alignment in subject<br /><code>send      </code>End of alignment in subject<br /><code>qseq      </code>Aligned part of query sequence<br /><code>sseq      </code>Aligned part of subject sequence<br /><code>evalue    </code>Expect value<br /><code>bitscore  </code>Bit score<br /><code>score     </code>Raw score<br /><code>length    </code>Alignment length<br /><code>pident    </code>Percentage of identical matches<br /><code>nident    </code>Number of identical matches<br /><code>mismatch  </code>Number of mismatches<br /><code>positive  </code>Number of positive-scoring matches<br /><code>gapopen   </code>Number of gap openings<br /><code>gaps      </code>Total number of gaps<br /><code>ppos      </code>Percentage of positive-scoring matches<br /><code>frames    </code>Query and subject frames separated by a '/'<br /><code>qframe    </code>Query frame<br /><code>sframe    </code>Subject frame<br /><code>btop      </code>Blast traceback operations (BTOP)<br /><code>staxids   </code>Subject Taxonomy ID(s), separated by a ';'<br /><code>sscinames </code>Subject Scientific Name(s), separated by a ';'<br /><code>scomnames </code>Subject Common Name(s), separated by a ';'<br /><code>sblastnames </code>Subject Blast Name(s), separated by a ';'   (in alphabetical order)<br /><code>sskingdoms  </code>Subject Super Kingdom(s), separated by a ';'     (in alphabetical order) <br /><code>stitle      </code>Subject Title<br /><code>salltitles  </code>All Subject Title(s), separated by a '&lt;&gt;'<br /><code>sstrand   </code>Subject Strand<br /><code>qcovs     </code>Query Coverage Per Subject<br /><code>qcovhsp   </code>Query Coverage Per HSP<br /><strong><br /><em>default values are:</em></strong><br /><code><code>-outfmt "</code>6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore"</code></p>
</div></div></div>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/43424/rest-api</guid>
	<pubDate>Mon, 04 Oct 2021 12:46:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/43424/rest-api</link>
	<title><![CDATA[REST API]]></title>
	<description><![CDATA[<h3 id="PSIBLASTHelpandDocumentation-RESTAPI">REST API</h3><p>The&nbsp;<a href="https://www.ebi.ac.uk/seqdb/confluence/pages/viewpage.action?pageId=68165098">Representational State Transfer (REST)</a>&nbsp;sample clients are provided for a number of programming languages. For details of how to use these clients,&nbsp;<a href="https://github.com/ebi-wp/webservice-clients">download</a>&nbsp;the client and run the program without any arguments.</p><div><table><colgroup><col><col><col></colgroup>
<thead>
<tr><th scope="col">
<div>Language</div>
</th><th scope="col">
<div>Download</div>
</th><th scope="col">
<div>Requirements</div>
</th></tr>
</thead>
<tbody>
<tr><th>Perl</th>
<td><a href="https://raw.githubusercontent.com/ebi-wp/webservice-clients/master/perl/psiblast.pl">psiblast.pl</a></td>
<td><a href="http://search.cpan.org/perldoc?LWP">LWP</a>&nbsp;and&nbsp;<a href="http://search.cpan.org/perldoc?XML::Simple">XML::Simple</a></td>
</tr>
<tr><th colspan="1">
<h4 id="PSIBLASTHelpandDocumentation-Python">Python</h4>
</th>
<td colspan="1">
<p><a href="https://raw.githubusercontent.com/ebi-wp/webservice-clients/master/python/psiblast.py">psiblast.py</a></p>
</td>
<td colspan="1"><a href="https://pypi.python.org/pypi/xmltramp2/3.0.10" title="https://pypi.python.org/pypi/xmltramp2/3.0.10">xmltramp2</a></td>
</tr>
</tbody>
</table></div><p>For details see&nbsp;<a href="https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/Environment+setup+for+REST+Web+Services">Environment setup for REST Web Services</a>&nbsp;and&nbsp;<a href="https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/Examples+for+Perl+REST+Web+Services+Clients">Examples for Perl REST Web Services Clients</a>&nbsp;pages.</p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36893/beap-blast-extension-and-assembly-program</guid>
	<pubDate>Mon, 11 Jun 2018 04:52:56 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36893/beap-blast-extension-and-assembly-program</link>
	<title><![CDATA[BEAP: Blast Extension and Assembly Program]]></title>
	<description><![CDATA[The Blast Extension and Assembly Program (BEAP) is a computer program that uses a short starting DNA fragment, often a EST or partial gene segment, as "primer", to recursively blast nucleotide databases in an attempt to obtain all sequences that overlaps, directly or indirectly, with the "primer" therefore help to "extend" the length of the original sequence for constructing a "full length" sequence for functional analysis, or at least to obtain neighboring regions of the segment for SNP discovery and linkage disequilibrium analysis. The confidence of assembling the resulting sequences is achieved by using a known genome, such as human genome, as a reference.
 
https://www.animalgenome.org/tools/beap/<p>Address of the bookmark: <a href="https://www.animalgenome.org/tools/beap/" rel="nofollow">https://www.animalgenome.org/tools/beap/</a></p>]]></description>
	<dc:creator>Shruti Paniwala</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/41956/blast-on-docker-google-cloud-amazon-cloud</guid>
	<pubDate>Thu, 09 Jul 2020 02:57:11 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/41956/blast-on-docker-google-cloud-amazon-cloud</link>
	<title><![CDATA[Blast on Docker, Google Cloud, Amazon Cloud]]></title>
	<description><![CDATA[<p>As announced in a&nbsp;<a href="https://ncbiinsights.ncbi.nlm.nih.gov/2019/07/16/the-blast-programs-and-databases-are-available-in-docker-and-cloud-ready/" target="_blank">previous post</a>, we offer a&nbsp;<a href="https://www.docker.com/" target="_blank">Docker</a>&nbsp;version of NCBI BLAST+ that you can use locally or on the&nbsp;<a href="https://cloud.google.com/" target="_blank">Google Cloud</a>&nbsp;where we have pre-loaded BLAST databases.&nbsp; We are happy to announce that the same functionality is now available on the&nbsp;<a href="https://aws.amazon.com/" target="_blank">Amazon Cloud</a>.&nbsp; In addition, we now offer 23 different BLAST databases on each cloud platform.<span style="text-decoration: underline;"></span><span style="text-decoration: underline;"></span></p><p>As mentioned before, working with BLAST+ in Docker and the cloud has several advantages:<span style="text-decoration: underline;"></span><span style="text-decoration: underline;"></span></p><ul>
<li>Docker manages installation and maintenance of the BLAST programs and databases.<span style="text-decoration: underline;"></span><span style="text-decoration: underline;"></span></li>
<li>Docker makes it is easier to integrate BLAST with other tools in your pipelines.<span style="text-decoration: underline;"></span><span style="text-decoration: underline;"></span></li>
<li>NCBI BLAST databases are pre-loaded now on the both the&nbsp;<a href="https://cloud.google.com/" target="_blank" title="Follow link">Google Cloud</a>&nbsp;and&nbsp;<a href="https://aws.amazon.com/" target="_blank" title="Follow link">Amazon Cloud</a>, providing fast access.<span style="text-decoration: underline;"></span><span style="text-decoration: underline;"></span></li>
</ul><p>You can also use the BLAST+ Docker image on any Docker-enabled platform, such as another cloud platform or on your local computer.<span style="text-decoration: underline;"></span><span style="text-decoration: underline;"></span></p><p>See the&nbsp;&nbsp;<a href="https://github.com/ncbi/blast_plus_docs" target="_blank" title="Follow link">BLAST+ in the Cloud</a>&nbsp;and&nbsp;&nbsp;<a href="https://github.com/ncbi/docker/wiki/Getting-BLAST-databases" target="_blank" title="Follow link">database information</a>&nbsp;documentation to get started.<span style="text-decoration: underline;"></span><span style="text-decoration: underline;"></span></p><p>If you have any questions, please email us at&nbsp;blast-help@ncbi.nlm.nih.gov</p><p>Source:<span>Dave Arndt</span></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36833/bfc-a-standalone-high-performance-tool-for-correcting-sequencing-errors-from-illumina-sequencing-data</guid>
	<pubDate>Thu, 31 May 2018 09:35:23 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36833/bfc-a-standalone-high-performance-tool-for-correcting-sequencing-errors-from-illumina-sequencing-data</link>
	<title><![CDATA[BFC: a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data]]></title>
	<description><![CDATA[BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes.

The BFC algorithm is a variant of the classical spectrum alignment algorithm introduced by Pevzner et al (2001). It uses an exhaustive search to find a k-mer path through a read that minimizes a heuristic objective function jointly considering penalties on correction, quality and k-mer support. This algorithm was first implemented in my fermi assembler and then refined a few times in fermi, fermi2 and now in BFC. In the k-mer counting phase, BFC uses a blocked bloom filter to filter out most singleton k-mers and keeps the rest in a hash table (Melsted and Pritchard, 2011). The use of bloom filter is how BFC is named, though other correctors such as Lighter and Bless actually rely more on bloom filter than BFC.

https://github.com/lh3/bfc<p>Address of the bookmark: <a href="https://github.com/lh3/bfc" rel="nofollow">https://github.com/lh3/bfc</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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