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<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/27799?offset=430</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42963/davi-deep-learning-based-tool-for-alignment-and-single-nucleotide-variant-identification</guid>
	<pubDate>Tue, 16 Mar 2021 05:41:33 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42963/davi-deep-learning-based-tool-for-alignment-and-single-nucleotide-variant-identification</link>
	<title><![CDATA[DAVI: Deep learning-based tool for alignment and single nucleotide variant identification]]></title>
	<description><![CDATA[<p>DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools used for bench-marking. We further demonstrate that while existing tools are based on data generated from a specific sequencing technology, the models proposed in DAVI are generic and can be used across different NGS technologies as well as across different species</p>
<p>https://iopscience.iop.org/article/10.1088/2632-2153/ab7e19/pdf</p><p>Address of the bookmark: <a href="https://github.com/gguptaiitd/NEAT" rel="nofollow">https://github.com/gguptaiitd/NEAT</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/17898/ensembl-77-has-been-released</guid>
	<pubDate>Sun, 05 Oct 2014 16:38:58 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/17898/ensembl-77-has-been-released</link>
	<title><![CDATA[Ensembl 77 has been released!]]></title>
	<description><![CDATA[<h3>New updates in e!77 !!</h3><ul>
<li>Updated&nbsp;<a href="http://e77.ensembl.org/Homo_sapiens/Info/Index" title="Human species page">human</a>&nbsp;gene set (GENCODE 21)</li>
<li>Updated <a href="http://e77.ensembl.org/Rattus_norvegicus/Info/Index">rat</a> gene set&nbsp;including manual annotation from HAVANA</li>
<li>New species:&nbsp;<a href="http://e77.ensembl.org/Chlorocebus_sabaeus/Info/Index">Vervet-African green monkey</a></li>
<li>Imported Transcript Support Levels (TSLs) from UCSC&nbsp;for&nbsp;<a href="http://e77.ensembl.org/Homo_sapiens/Info/Index">human</a>&nbsp;and&nbsp;<a href="http://e77.ensembl.org/Mus_musculus/Info/Index">mouse</a></li>
<li>Imported <a href="http://appris.bioinfo.cnio.es/" target="_blank" title="APPRIS">APPRIS</a> flag for&nbsp;<a href="http://e77.ensembl.org/Homo_sapiens/Info/Index">human</a> and <a href="http://e77.ensembl.org/Mus_musculus/Info/Index">mouse</a></li>
<li>Updated <a href="http://e77.ensembl.org/Poecilia_formosa/Info/Index" title="Amazon molly">Amazon molly</a> gene set</li>
</ul><p>Find more at http://www.ensembl.info/blog/2014/10/02/ensembl-77-has-been-released/</p>]]></description>
	<dc:creator>Seema Singh</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/33866/perlbrew-admin-free-perl-installation-management-tool</guid>
	<pubDate>Wed, 12 Jul 2017 03:53:08 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/33866/perlbrew-admin-free-perl-installation-management-tool</link>
	<title><![CDATA[Perlbrew: admin-free perl installation management tool.]]></title>
	<description><![CDATA[<p>perlbrew is an admin-free perl installation management tool. The latest version is 0.79, read the release note:&nbsp;<a href="https://perlbrew.pl/Release-0.79.html">Release 0.79</a>.&nbsp;</p>
<p>Copy &amp; Paste this line into your terminal:</p>
<pre><code>\curl -L https://install.perlbrew.pl | bash
</code></pre>
<p>Or, if your system does not have curl but something else:</p>
<pre><code># Linux
\wget -O - https://install.perlbrew.pl | bash

# FreeBSD
\fetch -o- https://install.perlbrew.pl | sh
</code></pre>
<p>If you prefer to install with cpan, there are two steps:</p>
<pre><code>sudo cpan App::perlbrew
perlbrew init
</code></pre>
<p>If it is installed with cpan, the perlbrew executable should be installed as&nbsp;<code>/usr/bin/perlbrew</code>&nbsp;or&nbsp;<code>/usr/local/bin/perlbrew</code>. For all users who want to use perlbrew, a prior&nbsp;<code>perlbrew init</code>&nbsp;needs to be executed.</p>
<p>The default perlbrew root directory is&nbsp;<code>~/perl5/perlbrew</code>, which can be changed by setting&nbsp;<code>PERLBREW_ROOT</code>environment variable before the installation and initialization. For more advanced installation process, please read&nbsp;<a href="http://metacpan.org/module/App::perlbrew">the perlbrew document</a>.</p>
<p>&nbsp;</p><p>Address of the bookmark: <a href="https://perlbrew.pl/" rel="nofollow">https://perlbrew.pl/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34528/cope-an-accurate-k-mer-based-pair-end-reads-connection-tool-to-facilitate-genome-assembly</guid>
	<pubDate>Wed, 06 Dec 2017 02:08:14 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34528/cope-an-accurate-k-mer-based-pair-end-reads-connection-tool-to-facilitate-genome-assembly</link>
	<title><![CDATA[COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly]]></title>
	<description><![CDATA[<p><span>An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30&times; simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, which is, respectively, 10 and 2% higher than the recently published tool FLASH. When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer errors and give a 14-fold improvement in the N50 measurement when compared with the contigs produced using unconnected reads.</span></p><p>Address of the bookmark: <a href="ftp://ftp.genomics.org.cn/pub/cope" rel="nofollow">ftp://ftp.genomics.org.cn/pub/cope</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/18380/jrfsrf-at-university-of-hyderabad</guid>
  <pubDate>Fri, 17 Oct 2014 01:55:44 -0500</pubDate>
  <link></link>
  <title><![CDATA[JRF/SRF at University of Hyderabad]]></title>
  <description><![CDATA[
<p>Applications are invited for the following post of Junior Research Fellow (temporary position coterminous with the project) under DBT funded research project on ““Understanding the functions of α1β1γ1/α2β1γ1 selective AMPK Modulators in dissecting the pharmacological role of these isozymes in metabolic diseases”</p>

<p>Qualified and interested candidates can send their curriculum vitae by e-mail to hr@drils.org on or before 27th October 2014 mention in the subject line of the mail the following code: AMPK-Biology.</p>

<p>Selected candidates will be called for a personal interview to Dr. Reddy’s Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad. The selected candidate is expected to report within two weeks from the date of selection to start work on the project.</p>

<p>Junior Research Fellowship (Molecular Modeling/Biology) for two years and Senior Research fellowship for one year</p>

<p>Junior Research Fellowship: Rs. 15,600/- (consolidated) per month for first two years.<br />Senior Research Fellowship: Rs. 18,200/-(consolidated) per month for the 3rd year.</p>

<p>Duration: The duration of the fellowship is for three years. However, the performance of the candidate will be reviewed after the completion of every year and the fellowship will be renewed only upon satisfactory performance.</p>

<p>Responsibilities:</p>

<p>1) Literature search.<br />2) Design, plan and execute experiments under the supervision of the scientist.<br />3) Provide scientific support to the scientist in his/her research activities.<br />4) Book keeping and maintenance of stocks and consumables.</p>

<p>Essential Qualifications:</p>

<p>Required: M.Sc. in Microbiology/Biotechnology/Bioinformatics or any other related branch of basic Sciences from a recognized university/institute with a consistent academic record of minimum 60% aggregate in all qualifying examinations. The candidate should be NET qualified for lectureship. The candidate should be motivated to work with dedication.</p>

<p>Desirable: expertise/experience in both Molecular Modeling and Molecular Biology.</p>

<p>Experience: 0-2 years in the areas of Molecular Modeling and/or Molecular Biology and cell biology and Biochemistry.</p>

<p>Preferable: Relevant research experience as evident from thesis/dissertation/project work.</p>

<p>Advertisement: http://www.ilsresearch.org/userfiles/Junior%20REsearch%20Fellowship%20-%20AMPK(Biology).pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34594/synima-synteny-imaging-tool</guid>
	<pubDate>Sun, 10 Dec 2017 17:03:48 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34594/synima-synteny-imaging-tool</link>
	<title><![CDATA[Synima: Synteny Imaging tool]]></title>
	<description><![CDATA[<p><span>Synteny Imaging tool (Synima) written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima &ndash; and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from&nbsp;</span><span><a href="https://github.com/rhysf/Synima"><span>https://github.com/rhysf/Synima</span></a></span><span>&nbsp;under the MIT License.</span></p><p>Address of the bookmark: <a href="https://github.com/rhysf/Synima" rel="nofollow">https://github.com/rhysf/Synima</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35885/multi-car-a-tool-of-contig-scaffolding-using-multiple-references</guid>
	<pubDate>Tue, 06 Mar 2018 16:39:41 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35885/multi-car-a-tool-of-contig-scaffolding-using-multiple-references</link>
	<title><![CDATA[Multi-CAR: a tool of contig scaffolding using multiple references]]></title>
	<description><![CDATA[<p><span>we design a simple heuristic method to further revise our single reference-based scaffolding tool CAR into a new one called Multi-CAR such that it can utilize multiple complete genomes of related organisms as references to more accurately order and orient the contigs of a draft genome. In practical usage, our Multi-CAR does not require prior knowledge concerning phylogenetic relationships among the draft and reference genomes and libraries of paired-end reads. To validate Multi-CAR, we have tested it on a real dataset composed of several prokaryotic genomes and also compared its accuracy performance with other multiple reference-based scaffolding tools Ragout and MeDuSa.&nbsp;</span></p><p>Address of the bookmark: <a href="http://genome.cs.nthu.edu.tw/Multi-CAR/" rel="nofollow">http://genome.cs.nthu.edu.tw/Multi-CAR/</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/18580/faculty-positions-at-central-university-of-punjab-bathinda</guid>
  <pubDate>Wed, 22 Oct 2014 10:45:37 -0500</pubDate>
  <link></link>
  <title><![CDATA[Faculty Positions at CENTRAL UNIVERSITY OF PUNJAB, BATHINDA]]></title>
  <description><![CDATA[
<p>Advertisement No. T/NT-01 (2014)</p>

<p>Faculty Positions<br />The Central University of Punjab (CUP), Bathinda will be having the Schools and Departments as given in Table-I. The University invites applications from eligible candidates for the posts of Professors (Pay Band Rs. 37400-67000 with AGP of Rs. 10, 000/-), Associate Professors (Pay Band Rs.37400-67000 with AGP of Rs. 9,000/-) and Assistant Professors (Pay Band Rs.15600-39100 with AGP of Rs. 6,000/-)</p>

<p>POSITION AVAILABLE IN THE AREA OF SPECIALIZTION</p>

<p>3. Bioinformatics,</p>

<p>Procedure to apply: Application forms along with API form complete in all respect along with necessary documents and application fee of Rs. 750/-. (Rs. 250/- for Scheduled Caste/Scheduled Tribe/Person with disabilities) should be sent to:</p>

<p>Registrar (Officiating)<br />Central University of Punjab<br />City Campus, Mansa Road<br />Bathinda-151 001</p>

<p>Application forms from the prospective candidates are accepted upto November 10, 2014.</p>

<p>Based on the qualification of the candidates and the need of the university, the applications received will be processed through appropriately constituted selection committees shortly. Minimum qualification can be relaxed in case of exceptionally outstanding candidate. For further details visit www.cup.ac.in; www.centralunipunjab.com; www.cup.edu.in</p>

<p>The candidate should download the application form available at website www.cup.ac.in;<br />www.centralunipunjab.com; and submit it complete in all respects on or before 10th November 2014.</p>

<p>Those who have applied earlier need to submit Academic Performance Index (API) form, 5 copies of Summary of the Application Form (available at: www.cup.ac.in; www.centralunipunjab.com and Updated CV if not updated recently (without application fee).</p>

<p>http://cup.edu.in/Faculty_details_and_general_instructions.pdf</p>

<p>http://cup.edu.in/Final%20Application%20and%20summary%20Sheet%20and%20Api%20form.pdf</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/opportunity/view/19020/jrf-in-bioinformatics-bioinformatics-centre-north-eastern-hill-university</guid>
  <pubDate>Thu, 06 Nov 2014 10:24:05 -0600</pubDate>
  <link></link>
  <title><![CDATA[JRF in Bioinformatics @ Bioinformatics Centre, North-Eastern Hill University]]></title>
  <description><![CDATA[
<p>Applications with complete bio-data are invited for JRF (3) and Project Assistant (1) in a DBT project "Next Generation Sequencing (NGS)-based de novo assembly of expressed transcripts and genome information of Orchids in North-East India" sanctioned for a period of 3 years.</p>

<p>Details are available at www.nehu.ac.in and www.bicnehu.ac.in.</p>

<p>Applications must reach the undersigned within 15 days from the date of publication of this advertisement.</p>

<p>Prof. Pramod Tandon. PI/Mr. Devendra Kumar Biswal (Co-PI)</p>
]]></description>
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