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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/30701?offset=480</link>
	<atom:link href="https://bioinformaticsonline.com/related/30701?offset=480" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	
<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25308/traineeship-at-biomedical-informatics-centre-pgimer-chandigarh</guid>
  <pubDate>Sun, 29 Nov 2015 03:04:27 -0600</pubDate>
  <link></link>
  <title><![CDATA[Traineeship at Biomedical Informatics Centre  PGIMER  Chandigarh]]></title>
  <description><![CDATA[
<p>Biomedical Informatics Centre</p>

<p>PGIMER</p>

<p>Chandigarh</p>

<p>invites application for a project dissertation program for students who have completed their first year of M.Sc. in Bioinformatics.</p>

<p>This is an exciting opportunity for Master's students to train in modern methods in Bioinformatics. The duration of the training will be four to six months, starting from January 2016.</p>

<p>Education: Pursuing M.Sc. Bioinformatics</p>

<p>Essential: Post graduate applicants should have completed their first year and should be in the third semester or first half of the second year.</p>

<p>Only students who are willing to spend a minimum period of 4 months to a maximum of six months, without any break, would be eligible for the program.</p>

<p>How to Apply: Candidates interested in the above project dissertation program should apply online. Send your CV, Scanned copy of letter of recommendation from Head of Institution along with Registration form in the given format should be sent to: info@bicpgi.org</p>

<p>Please mention clearly “Project dissertation &amp; your Name” in the Subject.</p>

<p>The last date for application is December 23, 2015</p>

<p>Note: Selected candidates may please note that the program is free of cost and would not provide any financial aid for transport and stay. Name of the selected candidates would be posted on the centre website by December 31, 2015.</p>

<p>Incomplete applications will be rejected.</p>

<p>For more information visit our website: http://bic-pgi.org/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39017/macse-multiple-alignment-of-coding-sequences-accounting-for-frameshifts-and-stop-codons</guid>
	<pubDate>Mon, 18 Feb 2019 04:21:50 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39017/macse-multiple-alignment-of-coding-sequences-accounting-for-frameshifts-and-stop-codons</link>
	<title><![CDATA[MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons]]></title>
	<description><![CDATA[<p>MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.</p>
<p>For further details about the underlying algorithm see the original publication:<br><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022594" target="_new">MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.<br>Vincent Ranwez, S&eacute;bastien Harispe, Fr&eacute;d&eacute;ric Delsuc, Emmanuel JP Douzery<br>PLoS One 2011, 6(9): e22594</a>.</p><p>Address of the bookmark: <a href="https://bioweb.supagro.inra.fr/macse/index.php?menu=releases" rel="nofollow">https://bioweb.supagro.inra.fr/macse/index.php?menu=releases</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25302/ra-bioinformatics-at-jamia-hamdard</guid>
  <pubDate>Sat, 28 Nov 2015 03:37:36 -0600</pubDate>
  <link></link>
  <title><![CDATA[RA Bioinformatics at Jamia Hamdard]]></title>
  <description><![CDATA[
<p>Research Associate, Bioinformatics Facility<br />Jamia Hamdard - New Delhi, Delhi<br />Research Associate, Bioinformatics Facility, Jamia Hamdard.<br />Emoluments: Rs. 22,000 + HRA 30%<br />Qualification: PhD or equivalent or having 3 years of research, teaching and design and development experience after M. Pharm./M.VSc./M.E./M.Tech. PhD in life sciences and related areas with experience in Bioinformatics may apply. Company Info.<br />Jamia Hamdard</p>

<p>Jamia Hamdard New Delhi - 110062 Additional Information States &amp; U.T State &amp; Union Territories Delhi How To Apply Apply Details<br />Last date of application: December 5, 2015 Web/Notification URL http://www.jamiahamdard.ac.in/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43952/elastic-blast</guid>
	<pubDate>Tue, 06 Sep 2022 18:14:57 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43952/elastic-blast</link>
	<title><![CDATA[Elastic BLAST !]]></title>
	<description><![CDATA[<p><a href="https://blast.ncbi.nlm.nih.gov/doc/elastic-blast/elasticblast.html?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=elasticblast-top3-20220823">ElasticBLAST</a>&nbsp;is a new way to&nbsp;<a href="https://blast.ncbi.nlm.nih.gov/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=elasticblast-top3-20220823">BLAST</a>&nbsp;large numbers of queries, faster and on the cloud. Here are the top three reasons you should use ElasticBLAST:</p>
<h6><strong><img src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2022/08/ElasticBLAST_Larger-e1659978198941.png?resize=150%2C120&amp;ssl=1" alt="" width="150" height="120" style="border: 0px;">1. ElasticBLAST can handle much LARGER queries!&nbsp;</strong></h6>
<p>ElasticBLAST can search query sets that have&nbsp;<em>hundreds to millions of sequences</em>&nbsp;and against BLAST databases of all sizes.</p>
<h6><span><img src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2022/08/ElasticBLAST_Faster.png?resize=150%2C120&amp;ssl=1" alt="" width="150" height="120" style="border: 0px;">2. ElasticBLAST is FASTER</span></h6>
<p>ElasticBLAST distributes your searches across multiple cloud instances to process them simultaneously. The ability to scale resources in this way allows you to process large numbers of queries in a shorter time than you could with BLAST+.</p>
<h6><img src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2022/08/ElasticBLAST_Easy.png?resize=150%2C120&amp;ssl=1" alt="" width="150" height="120" style="border: 0px;">3. ElasticBLAST is EASY to run on the cloud<strong><br></strong></h6>
<p>ElasticBLAST is easy to set up using our step-by-step instructions&nbsp;<span>(</span><a href="https://blast.ncbi.nlm.nih.gov/doc/elastic-blast/quickstart-aws.html?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=elasticblast-top3-20220823" target="_blank"><span><span>Amazon Web&nbsp;</span><span>Services (AWS)</span></span></a><span>,&nbsp;</span><a href="https://blast.ncbi.nlm.nih.gov/doc/elastic-blast/quickstart-gcp.html?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=elasticblast-top3-20220823" target="_blank"><span>Google Cloud Platform (GCP)</span></a><span><span>)</span>&nbsp;<span>and</span>&nbsp;<span>allows&nbsp;</span><span>you&nbsp;</span><span>to leverage the power of</span><span>&nbsp;the&nbsp;</span><span>cloud. Once configured, i</span><span>t</span>&nbsp;<span>manages the software and database installation, handles partitioning of the BLAST workload among the various instances, and deallocates cloud resources when the searches are done.</span></span></p>
<p><span><span>ElasticBLAST</span>&nbsp;<span>also&nbsp;</span><span>selects the instance (</span><span>i.e.,</span><span>&nbsp;machine) type for you based on database size. Of course, you can also choose the instance type manually if you prefer</span><span>.&nbsp;</span></span></p><p>Address of the bookmark: <a href="https://blast.ncbi.nlm.nih.gov/doc/elastic-blast/" rel="nofollow">https://blast.ncbi.nlm.nih.gov/doc/elastic-blast/</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42965/nucl2vec-local-alignment-of-dna-sequences-using-distributed-vector-representation</guid>
	<pubDate>Tue, 16 Mar 2021 05:45:44 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42965/nucl2vec-local-alignment-of-dna-sequences-using-distributed-vector-representation</link>
	<title><![CDATA[Nucl2Vec: Local alignment of DNA sequences using Distributed Vector Representation]]></title>
	<description><![CDATA[<p><span>We demonstrate a novel approach for</span><span>local alignment of DNA reads with respect to reference genome.</span><span>For this process we have used Skip-gram model for creating</span><span>encoding(Nucl2Vec) and k-nearest neighbor for the alignment.</span><span>With our new approach we have reduced computation cost for</span><span>local alignment , while achieving accuracy comparable to existing</span><span>defacto standard BWA-MEM tool.</span> </p>
<p><em>https://prakharg24.github.io/papers/401851.full.pdf</em></p><p>Address of the bookmark: <a href="https://prakharg24.github.io/papers/401851.full.pdf" rel="nofollow">https://prakharg24.github.io/papers/401851.full.pdf</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25504/uas-dharwad-assistant-professor</guid>
  <pubDate>Fri, 04 Dec 2015 21:06:23 -0600</pubDate>
  <link></link>
  <title><![CDATA[UAS Dharwad Assistant Professor]]></title>
  <description><![CDATA[
<p>UNIVERSITY OF AGRICULTURAL SCIENCES, DHARWAD</p>

<p>Applications are invited in the prescribed form for filling up the following posts of Teachers and Service Personnel from the candidates who are qualified as on the last date fixed for receipt of applications in the University of Agricultural Sciences, Dharwad.</p>

<p>I. ASSISTANT PROFESSOR CADRE (Scale of pay Rs.15600-39100 + AGP Rs. 6000) (UGC / ICAR pay-scales)</p>

<p>I. Re-notified posts:</p>

<p>9. Assistant Professor of Bioinformatics 1 GM-1</p>

<p>More Info : https://sites.google.com/a/uasd.in/recruitment/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34920/xmatchview-smith-waterman-alignment-visualization</guid>
	<pubDate>Thu, 28 Dec 2017 09:00:58 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34920/xmatchview-smith-waterman-alignment-visualization</link>
	<title><![CDATA[xmatchview: smith-waterman alignment visualization]]></title>
	<description><![CDATA[<p><span>xmatchview and xmatchview-conifer are imaging tools for comparing the synteny between DNA sequences. It allows users to align 2 DNA sequences in fasta format using cross_match and displays the alignment in a variety of image formats. xmatchview and xmatchview-conifer are written in python and run on linux and windows. They serve as visual tools for analyzing cross_match alignments. Cross_match (Green, P. (1994)&nbsp;</span><a href="http://www.phrap.org/">http://www.phrap.org</a><span>) uses an implementation of the Smith-Waterman algorithm for comparing DNA sequences that is sensitive.</span></p>
<p><span>http://www.bcgsc.ca/platform/bioinfo/software/xmatchview</span></p><p>Address of the bookmark: <a href="https://github.com/warrenlr/xmatchview" rel="nofollow">https://github.com/warrenlr/xmatchview</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25770/fellowship-doctoral-research-in-biomedical-genomics-including-statistical-genomics</guid>
  <pubDate>Sun, 20 Dec 2015 06:03:43 -0600</pubDate>
  <link></link>
  <title><![CDATA[Fellowship (Doctoral Research In Biomedical Genomics, Including Statistical Genomics)]]></title>
  <description><![CDATA[
<p>Fellowship (Doctoral Research In Biomedical Genomics, Including Statistical Genomics)<br />Eligibility : MSc(Bio-Chemistry, Bio-Informatics, Bio-Tech, Mathematics / Applied Mathematics, Stati, Zoology)<br />Location : Kolkata<br />Last Date : 31 Dec 2015<br />Hiring Process : Written-test</p>

<p>NO: 340/ESTB/ADMN/NIBMG/2015-16 <br />Doctoral Research In Biomedical Genomics, Including Statistical Genomics conduct National Institute of Biomedical Genomics (NIBMG)<br />Information For Students Interested To Pursue Doctoral Research In Biomedical Genomics, Including Statistical Genomics, At The National Institute Of Biomedical Genomics (Nibmg), Kalyan<br />Eligibility conditions for specific areas of research are :<br />Statistical Genomics : An applicant who wishes to pursue research in Statistical Genomics should hold a Master's degree (First class or equivalent) in a relevant discipline (Statistics, Mathematics, Bioinformatics, or a related discipline)<br />Biomedical Genomics : An applicant who wishes to pursue research in any area of biomedical genomics, other than statistical genomics, should hold a Master's degree (First class or equivalent) in a relevant discipline (Biochemistry, Biotechnology, Molecular Biology, Genetics, Zoology, Physiology, or a related discipline)<br />Fellowship : An applicant should have passed the NET conducted by CSIR/UGC/ICMR/DBT within the past ONE year AND should have been awarded a valid Junior Research Fellowship from CSIR, UGC, ICMR, DBT (Category-I only), DST (INSPIRE), NBHM. Preference will be given to candidates with demonstrable research training in the form of summer training or short-term courses in established research laboratories in preparation for a research career in biomedical sciences<br />How to apply<br />Online application will be accepted until 5 PM of December 31, 2015. A formal interview of the short-listed candidates will be held on January 12, 2016</p>

<p>More at http://www.nibmg.ac.in/?q=Career%20Opportunities</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36755/minialign-fast-and-accurate-alignment-tool-for-pacbio-and-nanopore-long-reads</guid>
	<pubDate>Thu, 24 May 2018 08:33:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36755/minialign-fast-and-accurate-alignment-tool-for-pacbio-and-nanopore-long-reads</link>
	<title><![CDATA[minialign: fast and accurate alignment tool for PacBio and Nanopore long reads]]></title>
	<description><![CDATA[Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.<p>Address of the bookmark: <a href="https://github.com/ocxtal/minialign" rel="nofollow">https://github.com/ocxtal/minialign</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<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>

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