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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/26587?offset=510</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36994/minimap2-a-versatile-pairwise-aligner-for-genomic-and-spliced-nucleotide-sequences</guid>
	<pubDate>Wed, 20 Jun 2018 07:55:29 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36994/minimap2-a-versatile-pairwise-aligner-for-genomic-and-spliced-nucleotide-sequences</link>
	<title><![CDATA[minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences]]></title>
	<description><![CDATA[git clone https://github.com/lh3/minimap2
cd minimap2 &amp;&amp; make
# long sequences against a reference genome
./minimap2 -a test/MT-human.fa test/MT-orang.fa &gt; test.sam
# create an index first and then map
./minimap2 -d MT-human.mmi test/MT-human.fa
./minimap2 -a MT-human.mmi test/MT-orang.fa &gt; test.sam
# use presets (no test data)
./minimap2 -ax map-pb ref.fa pacbio.fq.gz &gt; aln.sam       # PacBio genomic reads
./minimap2 -ax map-ont ref.fa ont.fq.gz &gt; aln.sam         # Oxford Nanopore genomic reads
./minimap2 -ax sr ref.fa read1.fa read2.fa &gt; aln.sam      # short genomic paired-end reads
./minimap2 -ax splice ref.fa rna-reads.fa &gt; aln.sam       # spliced long reads
./minimap2 -ax splice -k14 -uf ref.fa reads.fa &gt; aln.sam  # Nanopore Direct RNA-seq
./minimap2 -cx asm5 asm1.fa asm2.fa &gt; aln.paf             # intra-species asm-to-asm alignment
./minimap2 -x ava-pb reads.fa reads.fa &gt; overlaps.paf     # PacBio read overlap
./minimap2 -x ava-ont reads.fa reads.fa &gt; overlaps.paf    # Nanopore read overlap
# man page for detailed command line options
man ./minimap2.1<p>Address of the bookmark: <a href="https://github.com/lh3/minimap2" rel="nofollow">https://github.com/lh3/minimap2</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/12111/internship-program-with-arraygen-technolgies</guid>
  <pubDate>Sun, 22 Jun 2014 23:18:31 -0500</pubDate>
  <link></link>
  <title><![CDATA[Internship program with ArrayGen Technolgies]]></title>
  <description><![CDATA[
<p>Internship Program for Bioinformatics / Biotechnology Professionals Currently we offer positions to outstanding students interested in Next Generation Sequencing (NGS) data analysis. Applications are accepted throughout the year. Accepted students will be listed on web with their schedules. Accepted students can attend our future workshops and trainings freely at the specified venue.</p>

<p>Interested candidates may email their resume along with a cover letter to careers@arraygen.com</p>

<p>Official website: http://www.arraygen.com/</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37987/ropebwt2-incremental-construction-of-fm-index-for-dna-sequences</guid>
	<pubDate>Thu, 25 Oct 2018 04:48:54 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37987/ropebwt2-incremental-construction-of-fm-index-for-dna-sequences</link>
	<title><![CDATA[RopeBWT2: Incremental construction of FM-index for DNA sequences]]></title>
	<description><![CDATA[<p><span>RopeBWT2 is an tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This algorithm can be largely considered a mixture of&nbsp;</span><a href="http://dx.doi.org/10.1007/978-3-642-21458-5_20">BCR</a><span>&nbsp;and&nbsp;</span><a href="http://dfmi.sourceforge.net/">dynamic FM-index</a><span>. Nonetheless, ropeBWT2 is unique in that it may&nbsp;</span><em>implicitly</em><span>sort the input into reverse lexicographical order (RLO) or reverse-complement lexicographical order (RCLO) while building the index.</span></p><p>Address of the bookmark: <a href="https://github.com/lh3/ropebwt2" rel="nofollow">https://github.com/lh3/ropebwt2</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/12566/jrf-at-national-research-centre-on-plant-biotechnology</guid>
  <pubDate>Fri, 04 Jul 2014 13:36:02 -0500</pubDate>
  <link></link>
  <title><![CDATA[JRF at NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY]]></title>
  <description><![CDATA[
<p>NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY</p>

<p>New Delhi-110012</p>

<p>Walk in interview</p>

<p>Eligible candidates may appear for Walk-in interview for the temporary positions of JRF/SRF/ RA, in ICAR, DBT funded research projects. Positions are purely temporary in nature and are co-terminus with the projects. The initial appointment will be for maximum one year, which can be extended on the basis of assessment of the candidate performance and need in the project work (PI-Dr. N. K. Singh, National Professor).</p>

<p>Name of the</p>

<p>PI (Project)<br />	</p>

<p>Name of</p>

<p>Position<br />	</p>

<p>Number of</p>

<p>positions<br />	</p>

<p>Emoluments</p>

<p>Fixed per</p>

<p>month (Rs.)<br />	</p>

<p>Essential</p>

<p>Qualifications</p>

<p>DBT-“Physical Mapping and Sample sequencing of Wheat Chromosome 2A- International Wheat Genome Sequencing Consortium (India)”.</p>

<p>(Up to Nov,2014)</p>

<p>DBT- Identification and functional analysis of genes related to yield and biotic stresses (Up to Oct,2014)</p>

<p>NPTC-Central Facility<br />	</p>

<p>RA (Master)</p>

<p>JRF/SRF</p>

<p>Research Associate: One</p>

<p>Essential: MCA or M. Tech. (Bioinformatics and computer Science with 2 years experience in Database Management with</p>

<p>MySQL, Linux)</p>

<p>Desirable: Proficiency in handling of large biological databases</p>

<p>Age limit: Max. Age 35 years (Age of relaxation of 5 years for SC/ST&amp; woman. and 3 years for OBC). The interview will be held on 08 July, 2014 at 11 am at room no. 39, NRCPB, LBS Building, Pusa Campus, New Delhi-110012. The candidates must bring original certificates and four copies of biodata, and recent passport size photograph. No TA/DA would be given for the appearance in interview. Only the candidates having essential qualifications would be entertained for the interviews.</p>

<p>Advertisement:</p>

<p>www.nrcpb.org/sites/default/files/news%20paper%20advirtisment..docx</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38670/ltr-finder-an-efficient-program-for-finding-full-length-ltr-retrotranspsons-in-genome-sequences</guid>
	<pubDate>Sun, 13 Jan 2019 07:05:53 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38670/ltr-finder-an-efficient-program-for-finding-full-length-ltr-retrotranspsons-in-genome-sequences</link>
	<title><![CDATA[LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.]]></title>
	<description><![CDATA[<p>LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.</p>
<p>The Program first constructs all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then Smith-Waterman algorithm is used to adjust the ends of LTR pair candidates to get alignment boundaries. These boundaries are subject to re-adjustment using supporting information of TG..CA box and TSRs and reliable LTRs are selected. Next, LTR_FINDER tries to identify PBS, PPT and RT inside LTR pairs by build-in aligning and counting modules. RT identification includes a dynamic programming to process frame shift. For other protein domains, LTR_FINDER calls ps_scan (from PROSITE,&nbsp;<a href="http://www.expasy.org/prosite/">http://www.expasy.org/prosite/</a>) to locate cores of important enzymes if they occur.</p><p>Address of the bookmark: <a href="https://github.com/xzhub/LTR_Finder" rel="nofollow">https://github.com/xzhub/LTR_Finder</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/12988/guest-lecturer-molecular-biology-bioinformatics</guid>
  <pubDate>Wed, 23 Jul 2014 13:34:41 -0500</pubDate>
  <link></link>
  <title><![CDATA[Guest Lecturer - Molecular Biology &amp; Bioinformatics]]></title>
  <description><![CDATA[
<p>Adv. No. F.TU/ACA/GT-APP/01/14 Date: 07.07.2014</p>

<p>Faculty of Science</p>

<p>Essential Qualifications:</p>

<p>(i) Good academic record having at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed) at the Master’s Degree level in a relevant subject, from an Indian University, or an equivalent degree from an accredited foreign University.</p>

<p>(II) Besides fulfilling the above qualifications, the candidates must have cleared the National Eligibility Test (NET) conducted by the UGC, CSIR or similar test accredited by the UGC like SLET/SET.</p>

<p>(III) Notwithstanding anything contained in sub-clauses (i) and (ii) of clause 4.4.1 of UGC regulations 2010, candidates, who are, or have been awarded a Ph.D. Degree in accordance with the University Grants Commission (Minimum Standards and Procedure for Award of Ph.D. Degree) Regulations, 2009, shall be exempted from the requirement of the minimum eligibility condition of NET/ SLET/ SET for engagement of guest Teacher.</p>

<p>(IV) NET/ SLET/ SET shall also not be required for such Master’s Degree Programmes in discipline for which NET/ SLET/ SET is not conducted.</p>

<p>Application form along with detailed instructions can be downloaded from Tripura University website: www.tripurauniv.in. The duly filled in application forms complete in all respects may be sent so as to reach the Office of the Deputy Registrar Academic Branch, Tripura University, Suryamaninagar - 799022, Tripura on or before 31st July, 2014. The Candidates who responded against advertisement No. TU.REG/N-Advt./02/10 dated 20.02.2014 need not apply again.</p>

<p>For more info visit: http://www.tripurauniv.in/images/universitymedia/EmploymentNotification/Guest%20Teacher%20Advt.%20website_09072014.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39872/miropeats-discovers-regions-of-sequence-similarity-amongst-any-set-of-dna-sequences</guid>
	<pubDate>Mon, 26 Aug 2019 17:55:24 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39872/miropeats-discovers-regions-of-sequence-similarity-amongst-any-set-of-dna-sequences</link>
	<title><![CDATA[Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences]]></title>
	<description><![CDATA[<p><span>Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically. Sequence similarity searching is a very general tool that forms the basis of many different biological sequence analyses but it is limited by the verbosity of traditional alignment presentation styles. Miropeats enhances the utility of conventional DNA sequence comparisons when looking at long lengths of sequence similarity by summarizing extensive large scale sequence similarities on a single page of graphics. The latest version of Miropeats can be used as a general pairwise alignment program or in its traditional role sorting out a big mess of overlapping or similar regions.</span></p><p>Address of the bookmark: <a href="http://www.littlest.co.uk/software/bioinf/old_packages/miropeats/" rel="nofollow">http://www.littlest.co.uk/software/bioinf/old_packages/miropeats/</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/14215/the-8000-years-old-tibetian-gene-mutation</guid>
	<pubDate>Wed, 20 Aug 2014 21:57:44 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/14215/the-8000-years-old-tibetian-gene-mutation</link>
	<title><![CDATA[The 8000 years old Tibetian gene mutation !!!]]></title>
	<description><![CDATA[<p>A new study has provided insight into how gene mutation around 8,000 years ago helped Tibetans' to survive in the thin air on the Tibetan Plateau, where an average elevation is of 14,800 feet.<br /><br />A study led by University of Utah scientists is the first to find a genetic cause for the adaptation, a single DNA base pair change that dates back 8,000 years and demonstrate how it contributes to the Tibetans' ability to live in low oxygen conditions.</p><p>About 8,000 years ago, the gene EGLN1 changed by a single DNA base pair. Today, a relatively short time later on the scale of human history, 88 percent of Tibetans have the genetic variation, and it was virtually absent from closely related lowland Asians. The findings indicate the genetic variation endows its carriers with an advantage.<br /><br />In those without the adaptation, low oxygen caused their blood to become thick with oxygen-carrying red blood cells, an attempt to feed starved tissues, which could cause long-term complications such as heart failure. The researchers found that the newly identified genetic variation protected Tibetans by decreasing the over-response to low oxygen.</p><p>Reference: http://www.nature.com/nature/journal/v512/n7513/abs/nature13408.html</p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41493/coronavirus-resources</guid>
	<pubDate>Wed, 25 Mar 2020 17:11:33 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41493/coronavirus-resources</link>
	<title><![CDATA[Coronavirus Resources !]]></title>
	<description><![CDATA[<p><span>2019nCoVR features comprehensive integration of genomic and proteomic sequences as well as their metadata information from the GISAID, NCBI, NMDC and CNCB/NGDC. It also incorporates a wide range of relevant information including scientific literatures, news, and popular articles for science dissemination, and provides visualization functionalities for genome variation analysis results based on all collected 2019-nCoV strains.</span></p>
<p><span>Annotation</span></p>
<p><span><a href="https://bigd.big.ac.cn/ncov/variation/annotation">https://bigd.big.ac.cn/ncov/variation/annotation</a></span></p>
<p><span>Genome wharehouse&nbsp;</span></p>
<p><span><a href="https://bigd.big.ac.cn/gwh/browse/index">https://bigd.big.ac.cn/gwh/browse/index</a></span></p>
<p>Released Genome</p>
<p><a href="https://bigd.big.ac.cn/ncov/release_genome">https://bigd.big.ac.cn/ncov/release_genome</a></p>
<p>Download data&nbsp;</p>
<p><a href="ftp://download.big.ac.cn/Genome/Viruses/Coronaviridae/">ftp://download.big.ac.cn/Genome/Viruses/Coronaviridae/</a></p>
<p>Raw data</p>
<p><a href="https://bigd.big.ac.cn/gsa/browse/run/?tag=Coronaviridae">https://bigd.big.ac.cn/gsa/browse/run/?tag=Coronaviridae</a></p><p>Address of the bookmark: <a href="https://bigd.big.ac.cn/ncov/about" rel="nofollow">https://bigd.big.ac.cn/ncov/about</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/12936/assistant-professor-medical-bioinformatics</guid>
  <pubDate>Wed, 23 Jul 2014 05:00:38 -0500</pubDate>
  <link></link>
  <title><![CDATA[Assistant Professor - Medical Bioinformatics]]></title>
  <description><![CDATA[
<p>Advt. No : ME-I/A-IV/03/14</p>

<p>No.of Posts:01 (SC)</p>

<p>Pay Scale:</p>

<p>Pay Band of Rs.15600-39100 + Rs.6000/- GP +NPA @ 25% of Basic Pay +Learning Resource Allowance @ Rs.20,000/-P.A.+ Conveyance Allowance @ Rs. 1650/-P.M.+ Academic Allowance @ Rs.2500/- P.M. and other admissible allowances.</p>

<p>Qualifications:</p>

<p>Area of Specialization:-</p>

<p>Bioinformatics/Computational/Biology/Genomics/ Proteomics/ Structural Biology</p>

<p>1. Postgraduate qualification, e.g. Master’s Degree in Biotechnology/Bioinformatics/ Biophysics.</p>

<p>2. A Doctorate Degree of recognized University/Institute in a basic or allied Medical Science subject e.g. Medical Biotechnology/Biophysics. Bioinformatics/X-ray Crystallography/</p>

<p>Immunology/Structural Biology etc</p>

<p>Experience:</p>

<p>1.Minimum three years teaching and/or research experience in a recognized medical/research Institution in an allied medical subject after obtaining doctorate degree and preferably in Medical</p>

<p>Molecular Biology/ Biophysics/Structural Biology/Genomics and Clinical Proteomics/Computational Biology.</p>

<p>2. Minimum two publication with atleast one in international journal and atleast one as first author</p>

<p>Desirable:-</p>

<p>Consistently excellent scholastic/academic record, demonstrated ability to write grant proposal/(s) successfully, Post Doctoral training in a frontier area of medical Bioinformatics Research and of direct relevance to clinical diagnosis or patient care (preferably from a recognized top-ranking medical institution abroad)</p>

<p>Send your applications to O/O, Deputy Registrar, Recruitment &amp; Establishment Cell, University of Health Sciences, Rohtak by 08.7.2014</p>

<p>For more details,please visit website:http://pgimsrohtak.nic.in/2014%20AP%20Advt.pdf</p>
]]></description>
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