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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/32633?offset=370</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/31024/dagchainer-computing-chains-of-syntenic-genes-in-complete-genomes</guid>
	<pubDate>Fri, 17 Feb 2017 16:13:35 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/31024/dagchainer-computing-chains-of-syntenic-genes-in-complete-genomes</link>
	<title><![CDATA[DAGchainer: Computing Chains of Syntenic Genes in Complete Genomes]]></title>
	<description><![CDATA[<p>The DAGchainer software computes chains of syntenic genes found within complete genome sequences. As input, DAGchainer accepts a list of gene pairs with sequence homology along with their genome coordinates. Using a scoring function which accounts for the distance between neighboring genes on each DNA molecule and the BLAST E-value score between homologs, maximally scoring chains of ordered gene pairs are computed and reported. This algorithm can be used to mine large evolutionary conserved regions of genomes between two organisms. Alternatively, by examining colinear sets of homologous genes found within a single genome, segmental genome duplications can be revealed.</p>
<p>This software distribution includes both the DAGchainer utility and a Java-based graphical interface that allows the inputs and outputs to be navigated and interrogated dynamically.</p><p>Address of the bookmark: <a href="http://dagchainer.sourceforge.net/" rel="nofollow">http://dagchainer.sourceforge.net/</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/31251/bioinformatics-opening-at-icgeb-new-delhi</guid>
  <pubDate>Thu, 02 Mar 2017 04:16:36 -0600</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics opening at ICGEB NEW DELHI]]></title>
  <description><![CDATA[
<p>ICGEB NEW DELHI</p>

<p>Applications are invited for:</p>

<p>Junior Research Fellow, in a DBT funded project, is available in Translational Health Group, ICGEB, New Delhi</p>

<p>Qualifications:</p>

<p>Education: M.Sc. (preferably in Biotechnology, Life Sciences or Zoology, Chemistry, Bioinformatics). Candidates with hands on experience on GC-MS data acquisition and analysis will be given preference. Bioinformatics expertise required.</p>

<p>Fellowship: As per DBT guidelines.</p>

<p>Tenure: The position is purely on temporary basis with an initial tenure of six months and based on satisfactory performance may continue until the completion of the project.</p>

<p>Closing date for applications: 04/03/2017</p>

<p>Please send a "TWO PAGE" CV by email to:  th.icgeb@gmail.com on or before the last date.</p>

<p>Research Associate, in a DBT funded project, is available in Translational Health Group, ICGEB, New Delhi</p>

<p>Qualifications:</p>

<p>Education: Ph.D. (in Biology, Biotechnology, Chemistry, Bioinformatics). Candidates with hands on experience on GC-MS data acquisition and analysis will be given preference. </p>

<p>Fellowship: As per DBT guidelines.</p>

<p>Tenure: The position is purely on temporary basis with an initial tenure of six months and  based on satisfactory performance may continue until the completion of the project.</p>

<p>Closing date for applications: 04/03/2017</p>

<p>Please send a "TWO PAGE" CV by email to: th.icgeb@gmail.com on or before the last date.</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/31526/sequenceserver</guid>
	<pubDate>Fri, 10 Mar 2017 08:51:55 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/31526/sequenceserver</link>
	<title><![CDATA[sequenceserver]]></title>
	<description><![CDATA[<p><span>SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally or over the web.</span></p>
<p><span><span>More at&nbsp;</span><a href="http://sequenceserver.com/">http://sequenceserver.com</a><span>.</span></span></p><p>Address of the bookmark: <a href="https://github.com/wurmlab/sequenceserver" rel="nofollow">https://github.com/wurmlab/sequenceserver</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/31714/krona</guid>
	<pubDate>Wed, 22 Mar 2017 04:47:35 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/31714/krona</link>
	<title><![CDATA[Krona]]></title>
	<description><![CDATA[<p>Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an <a href="https://github.com/marbl/Krona/wiki/ExcelTemplate">Excel template</a> or <a href="https://github.com/marbl/Krona/wiki/KronaTools">KronaTools</a>, which includes support for several bioinformatics tools and raw data formats. The interactive charts are self-contained and can be viewed with any modern web browser (see <a href="https://github.com/marbl/Krona/wiki/Browser%20support">Browser support</a>).</p>
<p><a href="http://marbl.github.io/Krona/img/screen_mgrast.png"><img src="https://camo.githubusercontent.com/27b71b1f1832523723c3d14dec764e7ad098438c/687474703a2f2f6d6172626c2e6769746875622e696f2f4b726f6e612f696d672f7468756d625f6d67726173742e706e67" width="210" height="167" alt="image" style="border: 0px;"></a></p><p>Address of the bookmark: <a href="https://github.com/marbl/Krona/wiki" rel="nofollow">https://github.com/marbl/Krona/wiki</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32018/tmap-torrent-mapping-alignment-program-general-notes</guid>
	<pubDate>Sun, 02 Apr 2017 15:53:47 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32018/tmap-torrent-mapping-alignment-program-general-notes</link>
	<title><![CDATA[TMAP - torrent mapping alignment program General Notes]]></title>
	<description><![CDATA[<p>TMAP - torrent mapping alignment program <a href="https://github.com/iontorrent/TS/tree/master/Analysis/TMAP#general-notes"></a>General Notes</p>
<p>TMAP is a fast and accurate alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies.</p>
<ul>
<li>
<p>The latest TMAP is unsupported. To use a supported version, please see the TMAP version associated with a Torrent Suite release below.</p>
</li>
<li>
<p>Get the latest source code:</p>
<div>
<pre>git clone git://github.com/iontorrent/TMAP.git
 <span>cd</span> TMAP
 git submodule init
 git submodule update</pre>
</div>
</li>
</ul>
<p>https://github.com/iontorrent/TS/tree/master/Analysis/TMAP</p><p>Address of the bookmark: <a href="https://github.com/iontorrent/TS/tree/master/Analysis/TMAP" rel="nofollow">https://github.com/iontorrent/TS/tree/master/Analysis/TMAP</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32134/lifemap</guid>
	<pubDate>Mon, 10 Apr 2017 05:42:37 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32134/lifemap</link>
	<title><![CDATA[Lifemap]]></title>
	<description><![CDATA[<p><strong>Lifemap</strong> is an interactive tool to explore the WHOLE NCBI TAXONOMY. The concept used in <strong>Lifemap</strong> is similar to the one used in cartography with tools like Google Maps&copy; or Open Street Maps: exploring is done by zooming and panning.</p>
<div>
<p>&nbsp;The current tree contains ALL species present in NCBI taxonomy as of <span style="text-decoration: underline;">October 18th, 2016</span>: 1,135,169 species including 10,545 Archaea, 418,777 Bacteria and 705,847 Eukaryotes. The Lifemap tree is updated every two weeks.</p>
</div>
<p>&nbsp;All the nodes in the tree are clickable. This displays various information and options:</p>
<ul>
<li>The species name (and the associated common name if there is one)</li>
<li>The rank (kingdom, family, class, species...)</li>
<li>Ability to go to the corresponding node/species on NCBI web site (displayed in a new window)</li>
<li>Possibility to download the corresponding subtree in newick extended format</li>
<li>Possibilty to get the whole lineage from the current node/tip to the root of the tree.</li>
</ul><p>Address of the bookmark: <a href="http://lifemap-ncbi.univ-lyon1.fr/" rel="nofollow">http://lifemap-ncbi.univ-lyon1.fr/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32187/chromhmm-chromatin-state-discovery-and-characterization</guid>
	<pubDate>Wed, 19 Apr 2017 04:06:23 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32187/chromhmm-chromatin-state-discovery-and-characterization</link>
	<title><![CDATA[ChromHMM: Chromatin state discovery and characterization]]></title>
	<description><![CDATA[<p><span>ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks. ChromHMM is based on a multivariate Hidden Markov Model that explicitly models the presence or absence of each chromatin mark. The resulting model can then be used to systematically annotate a genome in one or more cell types. By automatically computing state enrichments for large-scale functional and annotation datasets ChromHMM facilitates the biological characterization of each state. ChromHMM also produces files with genome-wide maps of chromatin state annotations that can be directly visualized in a genome browser.&nbsp;</span><br><br></p>
<ul>
<li><a href="http://compbio.mit.edu/ChromHMM/ChromHMM.zip">ChromHMM software v1.12</a>&nbsp;(<a href="http://compbio.mit.edu/ChromHMM/versionlog.txt">version log</a>)</li>
<li><a href="http://compbio.mit.edu/ChromHMM/ChromHMM_manual.pdf">ChromHMM manual</a></li>
</ul><p>Address of the bookmark: <a href="http://compbio.mit.edu/ChromHMM/" rel="nofollow">http://compbio.mit.edu/ChromHMM/</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32420/fastq-format</guid>
	<pubDate>Wed, 03 May 2017 04:23:32 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32420/fastq-format</link>
	<title><![CDATA[Fastq format]]></title>
	<description><![CDATA[<p><strong>FASTQ format</strong>&nbsp;is a text-based&nbsp;<a href="https://en.wikipedia.org/wiki/File_format" title="File format">format</a>&nbsp;for storing both a biological sequence (usually&nbsp;<a href="https://en.wikipedia.org/wiki/Nucleotide_sequence" title="Nucleotide sequence">nucleotide sequence</a>) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single&nbsp;<a href="https://en.wikipedia.org/wiki/ASCII" title="ASCII">ASCII</a>&nbsp;character for brevity.</p>
<p>It was originally developed at the&nbsp;<a href="https://en.wikipedia.org/wiki/Wellcome_Trust_Sanger_Institute" title="Wellcome Trust Sanger Institute">Wellcome Trust Sanger Institute</a>&nbsp;to bundle a&nbsp;<a href="https://en.wikipedia.org/wiki/FASTA_format" title="FASTA format">FASTA</a>&nbsp;sequence and its quality data, but has recently become the&nbsp;<em>de facto</em>&nbsp;standard for storing the output of high-throughput sequencing instruments such as the&nbsp;<a href="https://en.wikipedia.org/wiki/Illumina_(company)" title="Illumina (company)">Illumina</a>&nbsp;Genome Analyzer.<sup id="cite_ref-Cock2009_1-0"><a href="https://en.wikipedia.org/wiki/FASTQ_format#cite_note-Cock2009-1">[1]</a></sup></p><p>Address of the bookmark: <a href="https://en.wikipedia.org/wiki/FASTQ_format" rel="nofollow">https://en.wikipedia.org/wiki/FASTQ_format</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/32496/bioinformatician-at-23andme</guid>
  <pubDate>Sat, 06 May 2017 17:57:39 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatician at 23andMe]]></title>
  <description><![CDATA[
<p>23andMe’s mission is to help people access, understand, and benefit<br />from the human genome. We are a group of passionate individuals excited<br />to push the boundaries of what’s possible to help turn genetic insight<br />into better health and personal understanding.</p>

<p>Our Research Team prides itself on driving cutting edge, industrial-scale<br />science to make an impact that belies the team’s size, in an environment<br />and culture that fosters creativity, innovation, collaboration, and fun.</p>

<p>More than 80% of our customers consent to participate in research, and as<br />a result of their participation, we have one of the largest recontactable,<br />genotyped, and phenotyped research cohorts in the world. The scope and<br />breadth of our vision means that most of the methods and tools necessary<br />to unlock the potential of this unique resource for discovery have yet<br />to be developed.</p>

<p>Our science has garnered the respect of many members of the<br />broader scientific community. For a list of our publications, see<br />www.23andme.com/publications/for-scientists/.</p>

<p>Join us! Visit our Careers page (www.23andMe.com/careers) to learn more<br />about these open positions:</p>

<p>•	Scientist, Research Communications<br />•	Bioinformaticist<br />•	Computational Biologist, Ancestry R&amp;D<br />•	Scientist/Senior Scientist, Statistical Genetics<br />•	Scientist/Senior Scientist, Survey Methodology<br />•	Scientist/Senior Scientist, Health R&amp;D<br />•	Senior Computational Biologist<br />•	Biostatistician</p>

<p>pfontanillas@23andme.com</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/32716/jrfsrf-project-assistant-ii-recruitment-in-national-agri-food-biotechnology-institute-nabi</guid>
  <pubDate>Mon, 15 May 2017 05:37:52 -0500</pubDate>
  <link></link>
  <title><![CDATA[JRF/SRF / Project Assistant-II recruitment in National Agri-Food Biotechnology Institute (NABI)]]></title>
  <description><![CDATA[
<p>National Agri-Food Biotechnology Institute<br />ADVT. No: 2017-Researcher (02)</p>

<p>JRF/SRF / Project Assistant-II recruitment in National Agri-Food Biotechnology Institute (NABI)</p>

<p>Essential Qualification: According to the DST (DST OM No.SR/S9/Z-09/2012 dated 21.10.2014) Post Graduate degree in basic science(M.Sc) in Bioinformatics/Computational Biology/Systems Biology/Information Technology with NET or Graduate degree in professional course with NET or Post Graduate Degree (M.Tech) in professional course in Bioinformatics/Computational Biology/Systems Biology/Information Technology. Desirable qualification/skills: 1) Should be proficient in programming in Perl/Python/R language etc. 2) Should have knowledge and skills for data mining in biological sequence database . sequence analysis tools/packages, NGS Analysis . 3) Should have knowledge and skills to work in linux environment and write shell scripts.</p>

<p>Age : 28 years</p>

<p>Hiring Process : Written-test<br />Job Role : Research/JRF/SRF<br />How to apply</p>

<p>Application should be sent to Administrative officer, National Agri-Food Biotechnology Institute, Knowledge City, Sector-81, Mohali so as to reach latest by 30.05.2017 before 5:30 pm.</p>

<p>More at http://www.nabi.res.in/Vacancies/NABI/ResearchFellowships/JRFSRFRA/2017/ADVT.%20No%202017Researcher%20(02)/ApplicationForm.pdf</p>
]]></description>
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