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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/29384?offset=1520</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42923/flanker</guid>
	<pubDate>Sat, 27 Feb 2021 22:04:53 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42923/flanker</link>
	<title><![CDATA[Flanker]]></title>
	<description><![CDATA[<p><span>Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of&nbsp;<span>mobile genetic elements (</span>MGEs) without prior knowledge of their structure.&nbsp;<span>Flanker can be flexibly parameterised to finetune outputs by characterising upstream and downstream regions separately and investigating variable lengths of flanking sequence.</span></span></p>
<p><span><img src="https://github.com/wtmatlock/flanker/raw/main/docs/frontpage.png" alt="image" style="border: 0px;"></span></p><p>Address of the bookmark: <a href="https://github.com/wtmatlock/flanker" rel="nofollow">https://github.com/wtmatlock/flanker</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/10182/biocodesbioscripts</guid>
	<pubDate>Tue, 22 Apr 2014 20:53:33 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/10182/biocodesbioscripts</link>
	<title><![CDATA[BioCodes/BioScripts]]></title>
	<description><![CDATA[<p>Over the years most bioinformatics people amass a collection of small utility scripts which make their lives easier. Too often they are kept either in private repositories or as part of a public collection to which noone else can contribute. Biocode is a curated repository of general-use utility scripts.</p>
<p>Algorithms scripts @ https://github.com/jschendel/bioinformatics-algorithms-coursera</p><p>Address of the bookmark: <a href="https://github.com/jorvis/biocode" rel="nofollow">https://github.com/jorvis/biocode</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43088/iva-accurate-de-novo-assembly-of-rna-virus-genomes</guid>
	<pubDate>Wed, 23 Jun 2021 07:51:59 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43088/iva-accurate-de-novo-assembly-of-rna-virus-genomes</link>
	<title><![CDATA[IVA: accurate de novo assembly of RNA virus genomes]]></title>
	<description><![CDATA[<p>IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 sequenced samples from human immunodeficiency virus-1 or influenza-virus-infected people and demonstrated that IVA outperforms all other virus de novo assemblers.</p>
<p><strong> Availability and implementation: </strong> The software runs under Linux, has the GPLv3 licence and is freely available from http://sanger-pathogens.github.io/iva</p>
<p>https://pubmed.ncbi.nlm.nih.gov/25725497/</p><p>Address of the bookmark: <a href="https://github.com/sanger-pathogens/iva" rel="nofollow">https://github.com/sanger-pathogens/iva</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/10380/ra-at-alagappa-university</guid>
  <pubDate>Sun, 04 May 2014 23:33:15 -0500</pubDate>
  <link></link>
  <title><![CDATA[RA at ALAGAPPA UNIVERSITY]]></title>
  <description><![CDATA[
<p>DEPARTMENT OF BIOTECHNOLOGY<br />(UGC SAP and DST-FIST &amp; PURSE Sponsored Department)<br />ALAGAPPA UNIVERSITY<br />(A State University Accredited by NAAC with „A‟ Grade)<br />Karaikudi - 630 004, India</p>

<p>WALK IN INTERVIEW</p>

<p>A walk-in Interview for the following position tenable at the Bioinformatics Infrastructure Facility (BIF), Department of Biotechnology, Alagappa University will be held at the Department of Biotechnology, Alagappa University, Karaikudi 630 003 on 15.05.2014 (Thursday) at 01:00 PM. This national facility is funded by the Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi. The main objectives of the Centre involve teaching and research activities in bioinformatics/biotechnology.</p>

<p>RA (One Post):</p>

<p>Salary : Rs. 11000 p.m. plus admissible HRA</p>

<p>Qualification: M.Sc., in Bioinformatics/Biotechnology/Biophysics/Biochemistry/ Life Sciences</p>

<p>Interested candidates are encouraged to send their Curriculum Vitae by email to “sk_pandian@rediffmail.com” in advance. On the day of interview, the candidates must produce original certificates in proof of their educational qualification and experience and a recommendation letter from the Head of the Department/Institution where last studied/worked. Candidates who have already passed the required Degree alone are eligible to appear for interview. No TA&amp;DA will be given for attending the interview.</p>

<p>Advertisement: http://www.alagappabiotech.org/Walk%20in%20interview.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43364/ragtag-a-collection-of-software-tools-for-scaffolding-and-improving-modern-genome-assemblies</guid>
	<pubDate>Sat, 11 Sep 2021 00:28:14 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43364/ragtag-a-collection-of-software-tools-for-scaffolding-and-improving-modern-genome-assemblies</link>
	<title><![CDATA[RagTag: a collection of software tools for scaffolding and improving modern genome assemblies]]></title>
	<description><![CDATA[<p>RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include:</p>
<ul>
<li>Homology-based misassembly&nbsp;<a href="https://github.com/malonge/RagTag/wiki/correct">correction</a></li>
<li>Homology-based assembly&nbsp;<a href="https://github.com/malonge/RagTag/wiki/scaffold">scaffolding</a>&nbsp;and&nbsp;<a href="https://github.com/malonge/RagTag/wiki/patch">patching</a></li>
<li>Scaffold&nbsp;<a href="https://github.com/malonge/RagTag/wiki/merge">merging</a></li>
</ul><p>Address of the bookmark: <a href="https://github.com/malonge/RagTag" rel="nofollow">https://github.com/malonge/RagTag</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/10459/associate-professor-bio-informatics-at-university-of-allahabad-in-allahabad</guid>
  <pubDate>Wed, 07 May 2014 00:26:53 -0500</pubDate>
  <link></link>
  <title><![CDATA[Associate Professor - Bio-Informatics at University of Allahabad in Allahabad]]></title>
  <description><![CDATA[
<p>No of vacancies: 01</p>

<p>Pay scale: Pay Band of Rs. 37400-67000 with AGP of Rs. 9000.</p>

<p>i. Educational Qualification: Good academic record with a Ph.D. Degree in the concerned/allied/relevant disciplines.</p>

<p>ii. A Master's Degree with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed).</p>

<p>iii. A minimum of eight years of experience of teaching and/or research in an academic/research position equivalent to that of Assistant Professor in a University, College or Accredited Research Institution/industry excluding the period of Ph.D. research with evidence of published work and a minimum of 5 publications as books and/or research/policy papers.</p>

<p>iv. Contribution to educational innovation, design of new curricula and courses, and technology - mediated teaching learning process with evidence of having guided doctoral candidates and research students.</p>

<p>v. A minimum score as stipulated in the Academic Performance Indicator (API) based Performance Based Appraisal System (PBAS), set out in UGC Regulation.</p>

<p>Download application form from website: http://www.allduniv.ac.in/</p>

<p>Send your application to the Registrar, University of Allahabad, Allahabad-211002 (U.P.) on or before 30th April 2014</p>

<p>For more details: http://www.allduniv.ac.in/images/adv/backlog/advt-details.pdf OR http://www.allduniv.ac.in/images/news/extension-notice.pdf</p>

<p>Last Apply Date: 30 May 2014</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43641/refseq-viraal-genome-sequences</guid>
	<pubDate>Sat, 11 Dec 2021 08:35:18 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43641/refseq-viraal-genome-sequences</link>
	<title><![CDATA[Refseq viraal genome sequences !]]></title>
	<description><![CDATA[<p>List of all viruses on NCBI&nbsp;</p>
<p>https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/</p><p>Address of the bookmark: <a href="https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/" rel="nofollow">https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/10664/dna-replication-process-3d-animation</guid>
	<pubDate>Sat, 10 May 2014 04:41:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/10664/dna-replication-process-3d-animation</link>
	<title><![CDATA[DNA Replication Process [3D Animation]]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/27TxKoFU2Nw" frameborder="0" allowfullscreen></iframe>See an organised list of all the animations: http://doctorprodigious.wordpress.com/hd-animations/]]></description>
	
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43722/crossmap-program-for-genome-coordinates-conversion-between-different-assemblies</guid>
	<pubDate>Tue, 25 Jan 2022 17:59:32 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43722/crossmap-program-for-genome-coordinates-conversion-between-different-assemblies</link>
	<title><![CDATA[CrossMap: program for genome coordinates conversion between different assemblies]]></title>
	<description><![CDATA[<p><span>CrossMap is a program for genome coordinates conversion between&nbsp;</span><em>different assemblies</em><span>&nbsp;(such as&nbsp;</span><a href="http://www.ncbi.nlm.nih.gov/assembly/2928/">hg18 (NCBI36)</a><span>&nbsp;&lt;=&gt;&nbsp;</span><a href="http://www.ncbi.nlm.nih.gov/assembly/2758/">hg19 (GRCh37)</a><span>). It supports commonly used file formats including&nbsp;</span><a href="https://samtools.github.io/hts-specs/SAMv1.pdf">BAM</a><span>,&nbsp;</span><a href="https://en.wikipedia.org/wiki/CRAM_(file_format)">CRAM</a><span>,&nbsp;</span><a href="https://en.wikipedia.org/wiki/SAM_(file_format)">SAM</a><span>,&nbsp;</span><a href="https://genome.ucsc.edu/goldenPath/help/wiggle.html">Wiggle</a><span>,&nbsp;</span><a href="https://genome.ucsc.edu/goldenPath/help/bigWig.html">BigWig</a><span>,&nbsp;</span><a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format1">BED</a><span>,&nbsp;</span><a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format3">GFF</a><span>,&nbsp;</span><a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format4">GTF</a><span>,&nbsp;</span><a href="https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/">MAF</a><span>&nbsp;</span><a href="https://samtools.github.io/hts-specs/VCFv4.2.pdf">VCF</a><span>, and&nbsp;</span><a href="https://sites.google.com/site/gvcftools/home/about-gvcf">gVCF</a><span>.</span></p><p>Address of the bookmark: <a href="http://crossmap.sourceforge.net/" rel="nofollow">http://crossmap.sourceforge.net/</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/10748/bioinformatics-phd-at-cuk-kerala</guid>
  <pubDate>Sat, 10 May 2014 20:21:22 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics PhD at CUK Kerala]]></title>
  <description><![CDATA[
<p>Applications are invited from highly motivated students (UGC-CSIR-JRF) with a background in Genomics/ Biotechnology/ Molecular Microbiology/ Biochemistry and Bioinformatics to pursue research leading to Ph.D. in the following areas;</p>

<p>    1. Cancer Genomics</p>

<p>    2. Microbial Genetics and Metagenomics</p>

<p>    3. Human Infective Diseases</p>

<p>    4. Computational Drug Design</p>

<p>Interested candidates may apply to Dr. Ranjith N. Kumavath, Assistant Professor &amp; Head, Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Padannakad (PO), Nileshwar, Kasaragod-671328,Kerala. Email: RNkumavath@gmail.com</p>
]]></description>
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