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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/28915?offset=1190</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38515/genome-annotation-using-maker-tutorial</guid>
	<pubDate>Thu, 20 Dec 2018 17:39:23 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38515/genome-annotation-using-maker-tutorial</link>
	<title><![CDATA[Genome Annotation using MAKER tutorial !]]></title>
	<description><![CDATA[<p><a href="http://www.yandell-lab.org/software/maker.html">MAKER</a><span>&nbsp;is a great tool for annotating a reference genome using empirical and&nbsp;</span><em>ab initio</em><span>gene predictions.&nbsp;</span><a href="http://gmod.org/wiki/Main_Page">GMOD</a><span>, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a&nbsp;</span><em>de novo</em><span>&nbsp;genome annotation for&nbsp;</span><em>Boa constrictor</em><span>&nbsp;in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.</span></p><p>Address of the bookmark: <a href="https://www.biostars.org/p/261203/" rel="nofollow">https://www.biostars.org/p/261203/</a></p>]]></description>
	<dc:creator>Shruti Paniwala</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/17894/faculty-position-at-national-institute-of-technology-rourkela</guid>
  <pubDate>Sun, 05 Oct 2014 15:45:13 -0500</pubDate>
  <link></link>
  <title><![CDATA[FACULTY POSITION at NATIONAL INSTITUTE OF TECHNOLOGY, ROURKELA]]></title>
  <description><![CDATA[
<p>NIT, Rourkela, an institute of national importance under Ministry of HRD, Govt. of India invites applications from Indian nationals possessing excellent academic background along with commitment to quality teaching and research for faculty positions at the level of Professor, Associate Professor and Assistant Professor in most branches of Engineering, Science, Management and Humanities as per following table:-</p>

<p>    1 Asst. Professor (on Pre-Ph.D. Contract)</p>

<p>    2 Asst. Professor (on Contract)</p>

<p>    3 Asst. Professor</p>

<p>    4 Associate Professor</p>

<p>    5 Professor</p>

<p>Life Sciences:-</p>

<p>    i)Biochemistry and Molecular Biology; ii)Cell and Developmental Biology; iii)Immunology and Molecular Medicine; (iv) Microbiology and Ecology (v)Bioinformatics Group; vi)Biophysical Sciences</p>

<p>HOW TO APPLY:-</p>

<p>a. Candidates willing to apply for one or more posts are requested to apply online at “http://www.nitrkl.ac.in/ JOBS &amp; TENDERS /Faculty Position” .<br />b. Persons employed in Government and Semi-Government organizations may apply directly against the standing advertisement. For this the application should be completed online. The printout of the application generated online should be submitted through employer if shortlisted for interview.<br />c. The online application can be filled in multiple sessions.<br />d. Candidates are required to check the Institute website from time to time for latest information, application status call for interview, change of dates and final results.<br />e. Applications shall be received online only. Please do not send application or CV against this advertisement by email or letter mail.</p>

<p>More Info: http://nitrkl.ac.in/Jobs_Tenders/1FacultyPosition/Default.aspx</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38801/genome-assembly-forensics-finding-the-elusive-mis-assembly</guid>
	<pubDate>Sat, 26 Jan 2019 18:02:01 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38801/genome-assembly-forensics-finding-the-elusive-mis-assembly</link>
	<title><![CDATA[Genome assembly forensics: finding the elusive mis-assembly]]></title>
	<description><![CDATA[<p><span>We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline, called&nbsp;</span><em>amosvalidate</em><span>. We demonstrate the application of our pipeline in both bacterial and eukaryotic genome assemblies, and highlight several assembly errors in both draft and finished genomes. The software described is compatible with common assembly formats and is released, open-source, at&nbsp;</span><a href="http://amos.sourceforge.net/" target="_blank">http://amos.sourceforge.net</a><span>.</span></p>
<p>https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2397507/&nbsp;</p>
<p>http://amos.sourceforge.net/wiki/index.php/AMOS</p><p>Address of the bookmark: <a href="http://amos.sourceforge.net/wiki/index.php/AMOS" rel="nofollow">http://amos.sourceforge.net/wiki/index.php/AMOS</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39626/geval-genome-evaluation-browser</guid>
	<pubDate>Tue, 18 Jun 2019 05:39:08 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39626/geval-genome-evaluation-browser</link>
	<title><![CDATA[gEVAL: Genome Evaluation Browser]]></title>
	<description><![CDATA[<p>The&nbsp;<strong>gEVAL Browser</strong>&nbsp;allows the evaluation of genome assemblies through its tools and pre-computed analyses.</p>
<p>The strength of this browser is the ability to navigate an up to date assembly and identify problematic regions and assist in strategizing potential solutions for these issues.</p>
<p>This facilitates the improvement of overall assemblies to a &ldquo;gold&rdquo; standard for release as reference genomes</p><p>Address of the bookmark: <a href="https://geval.sanger.ac.uk/index.html" rel="nofollow">https://geval.sanger.ac.uk/index.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/22318/research-fellows-at-csir-institute-of-himalayan-bioresource-technology-palampur-himachal-pradesh</guid>
  <pubDate>Tue, 19 May 2015 07:17:32 -0500</pubDate>
  <link></link>
  <title><![CDATA[Research Fellows at  CSIR - Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh]]></title>
  <description><![CDATA[
<p>CSIR - Institute of Himalayan Bioresource Technology 2 vacancies of Project Fellow</p>

<p>Name of the Post: Project Fellow</p>

<p>No. of the Post: 02 Two</p>

<p>Salary: Rs. 12000/- per month or Rs. 14000/- per month</p>

<p>Age Limit: Max. 28 years as on 10.06.2015 and relaxation as per rules</p>

<p>Required Job Profile:</p>

<p>Candidate must possess first class B.Tech. in bioinformatics or computational biology OR M.Sc. in bioinformatics or computational biology with fifty five percent marks OR M.Tech. in bioinformatics or computational biology with fifty five percent marks.</p>

<p>How to apply:</p>

<p>Eligible and interested candidates should need to appear for walk-in interview on 10.06.2015 at 9:00 am at the above mentioned address.</p>

<p>Refer to http://www.ihbt.res.in/recruit/AdvtNo7_2015.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40573/de-novo-genome-assembly-for-illumina-data</guid>
	<pubDate>Mon, 20 Jan 2020 05:13:29 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40573/de-novo-genome-assembly-for-illumina-data</link>
	<title><![CDATA[De novo Genome Assembly for Illumina Data]]></title>
	<description><![CDATA[<p>Written and maintained by <a href="mailto:simon.gladman@unimelb.edu.au">Simon Gladman</a> - Melbourne Bioinformatics (formerly VLSCI)</p>
<p>Protocol Overview / Introduction</p>
<p>In this protocol we discuss and outline the process of de novo assembly for small to medium sized genomes.</p>
<p>https://www.melbournebioinformatics.org.au/tutorials/tutorials/assembly/assembly-protocol/</p><p>Address of the bookmark: <a href="https://www.melbournebioinformatics.org.au/tutorials/tutorials/assembly/assembly-protocol/" rel="nofollow">https://www.melbournebioinformatics.org.au/tutorials/tutorials/assembly/assembly-protocol/</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/18384/big-genomic-data-on-google-cloud-platform</guid>
	<pubDate>Fri, 17 Oct 2014 02:16:00 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/18384/big-genomic-data-on-google-cloud-platform</link>
	<title><![CDATA[Big genomic data on Google Cloud Platform]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/ExNxi_X4qug" frameborder="0" allowfullscreen></iframe>As the cost of DNA sequencing has dropped, the volume of data produced has risen into the petabytes. Google is working with the genomics community to define a standard API for working with big genomic data sets in the cloud. Building on Google Cloud Platform, we show how to store, process, explore and share genomic data using technologies like BigQuery, AppEngine MapReduce, R and more.]]></description>
	
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41691/genobuntu-package-for-next-generation-sequencing-and-genome-assembly</guid>
	<pubDate>Mon, 18 May 2020 16:47:56 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41691/genobuntu-package-for-next-generation-sequencing-and-genome-assembly</link>
	<title><![CDATA[Genobuntu: Package for Next Generation Sequencing and Genome Assembly]]></title>
	<description><![CDATA[<div>
<p>Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.<br><br>Commonly used biological software and example script files for different assembly pipelines have also been provided, where the example script files can be updated to suit one&rsquo;s experimental needs. Genobuntu attempts to reduce the amount of time and energy needed to build software workstations and it can also act as a good teaching source for a class room setting.<br><br>Therefore, Genobuntu offers a well-tailored environment for both novices and experts working in the field of genome assembly.</p>
</div>
<div>
<h3>Features</h3>
<ul>
<li>Velvet</li>
<li>MiB</li>
<li>SSAKE</li>
<li>EULER</li>
<li>VCAKE</li>
<li>ABySS</li>
<li>ALLPATHS</li>
<li>Celera</li>
<li>SHARCGS</li>
<li>Allpaths</li>
<li>IDBA</li>
<li>TAIPAN</li>
<li>Edena</li>
<li>SOAPdenovo</li>
<li>Maq</li>
<li>IDBA-UD</li>
<li>No. of Reads present in the Ref. Seq.</li>
<li>ART NGS Reads Simulator</li>
<li>HiTEC, FASTQC</li>
<li>Minimum Description Length</li>
<li>SOAPaligner</li>
<li>Sequencing Read Archive Toolkit</li>
</ul>
</div><p>Address of the bookmark: <a href="https://sourceforge.net/projects/genobuntu/" rel="nofollow">https://sourceforge.net/projects/genobuntu/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/18579/cluster-innovation-center-university-of-delhi</guid>
  <pubDate>Wed, 22 Oct 2014 10:39:49 -0500</pubDate>
  <link></link>
  <title><![CDATA[CLUSTER INNOVATION CENTER @ UNIVERSITY OF DELHI]]></title>
  <description><![CDATA[
<p>Applications for Pre-selection of  candidates under ‘Institutions Mode’ for DST-ISPIRE Faculty in  Computational Biology/ Systems Biology/ Bioinformatics</p>

<p>Applications are invited for pre-selection  of candidates for Ministry of Science and Technology, Department of Science and Technology INSPIRE Faculty Scheme: a component of “Assured Opportunity for Research Career (AORC)” under INSPIRE in the area of computational Biology/Systems Biology/Bioinformatics.</p>

<p>Candidates having done their B.Tech/B.E.  and or M.Sc./M.Tech in Computer Science or Biotechnology and Ph.D. in Systems/ Computational Biology or Bioinformatics may apply in the following format prescribed by DST to the Director, Cluster Innovation Center, University Stadium, GC Narang Marg, University of Delhi, Delhi -11107. Detials of other qualification, age limits etc., please visit www.inspire-dst.gov.in.</p>

<p>Application on the prescribed format may be submitted by email to director@cic.du.ac.in before October 25, 2014. Selected candidates shall be called for an interview. The date, time and venue of the interview shall be informed by email/telephone. For more information about Cluster Innovation Center, please visit https://ducic.ac.in.</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44366/mitofinder</guid>
	<pubDate>Tue, 29 Aug 2023 02:13:01 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44366/mitofinder</link>
	<title><![CDATA[MitoFinder]]></title>
	<description><![CDATA[<p dir="auto">Allio, R., Schomaker-Bastos, A., Romiguier, J., Prosdocimi, F., Nabholz, B., &amp; Delsuc, F. (2020) Mol Ecol Resour. 20, 892-905. (<a href="https://doi.org/10.1111/1755-0998.13160">publication link</a>)</p>
<p dir="auto" style="text-align: center;"><a href="https://github.com/RemiAllio/MitoFinder/blob/master/image/logo.png" target="_blank"><img src="https://github.com/RemiAllio/MitoFinder/raw/master/image/logo.png" alt="Drawing" width="250" style="border: 0px;"></a></p>
<p dir="auto"><span>Mitofinder</span>&nbsp;is a pipeline to&nbsp;<span>assemble</span>&nbsp;mitochondrial genomes and&nbsp;<span>annotate</span>&nbsp;mitochondrial genes from trimmed read sequencing data.</p>
<p dir="auto"><span>MitoFinder</span>&nbsp;is also designed to&nbsp;<span>find</span>&nbsp;and&nbsp;<span>annotate</span>&nbsp;mitochondrial sequences in existing genomic assemblies (generated from Hifi/PacBio/Nanopore/Illumina sequencing data...)</p>
<p dir="auto"><span>MitoFinder</span>&nbsp;is distributed under the&nbsp;<a href="https://github.com/RemiAllio/MitoFinder/blob/master/License/LICENSE">license</a>.</p><p>Address of the bookmark: <a href="https://github.com/RemiAllio/MitoFinder" rel="nofollow">https://github.com/RemiAllio/MitoFinder</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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