<?xml version='1.0'?><rss version="2.0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:georss="http://www.georss.org/georss" xmlns:atom="http://www.w3.org/2005/Atom" >
<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/31064?offset=790</link>
	<atom:link href="https://bioinformaticsonline.com/related/31064?offset=790" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	
<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19600/studentship-at-nagaland-university</guid>
  <pubDate>Tue, 16 Dec 2014 01:35:00 -0600</pubDate>
  <link></link>
  <title><![CDATA[Studentship at Nagaland University]]></title>
  <description><![CDATA[
<p>Nagaland University<br />(A Central University Estd. By the Act of Parliament No. 35 of 1989)<br />Lumami 798 627, Nagaland<br />DBT Sponsored ‘Bioinformatics Infrastructure Facility’ Centre</p>

<p>Applications in plain paper are invited for the posts of (1) Traineeship (2 Nos.) and (2) Studentship – (2 Nos.) in the DBT funded-Bioinformatics Infrastructure Facility (BIF), Nagaland University, Lumami-798627, Nagaland. Details are given below. Interested candidates may submit the application along with self attested copies of certificates in support of the candidature to Prof. Chitta Ranjan Deb, Coordinator or Dr. L. N. Kakati, Deputy Coordinator, BIF Centre, Nagaland University, Lumami-798627, Nagaland on or before 15th January 2015.</p>

<p>The scanned application with relevant documents may be sent by email attachment to bifnulumami@gmail.com. Shortlisted candidates will be informed by email if called for interview. No TA/DA is admissible for attending the interview.</p>

<p>Traineeship (Two nos.)</p>

<p>    Post Graduate degree in any branch of Life Sciences from UGC recognized Universities</p>

<p>    Knowledge of computers and bioinformatics</p>

<p>    Rs.8000/- p.m. fixed.</p>

<p>    6 months</p>

<p>Studentship (Two nos.)</p>

<p>    Pursuing Post Graduate degree in any branch of Life Sciences from UGC recognized Universities</p>

<p>    Knowledge of computers and bioinformatics</p>

<p>    Rs.8000/- p.m. fixed.</p>

<p>    6 months</p>

<p>Terms and Conditions:</p>

<p>i) Applicants need to produce all original documents if call for interview.<br />ii) The posts are purely temporary and the appointment does not confer any entitlement or right over the job and will not be considered as formal service.<br />iii) No TA &amp; DA will be paid for appearing in the walk-in-interview.<br />iv) The stipend/salary amount is subject to the sanction of DBT, New Delhi.</p>

<p>Advertisement: http://www.nagauniv.org.in/files/BIF%20Advt.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34475/oxford-nanopore-sequencing-hybrid-error-correction-and-de-novo-assembly-of-a-eukaryotic-genome</guid>
	<pubDate>Wed, 29 Nov 2017 05:08:53 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34475/oxford-nanopore-sequencing-hybrid-error-correction-and-de-novo-assembly-of-a-eukaryotic-genome</link>
	<title><![CDATA[Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome]]></title>
	<description><![CDATA[<p><span>Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used for sequencing the S. cerevisiae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Nanocorr (</span><a href="https://github.com/jgurtowski/nanocorr">https://github.com/jgurtowski/nanocorr</a><span>) specifically for Oxford Nanopore reads, as existing packages were incapable of assembling the long read lengths (5-50kbp) at such high error rate (between ~5 and 40% error). With this new method we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: the contig N50 length is more than ten-times greater than an Illumina-only assembly (678kb versus 59.9kbp), and has greater than 99.88% consensus identity when compared to the reference. Furthermore, the assembly with the long nanopore reads presents a much more complete representation of the features of the genome and correctly assembles gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in the Illumina-only assembly.</span></p><p>Address of the bookmark: <a href="http://schatzlab.cshl.edu/data/nanocorr/" rel="nofollow">http://schatzlab.cshl.edu/data/nanocorr/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19729/senior-scientist-agricultural-bio-informatics-one-post</guid>
  <pubDate>Wed, 24 Dec 2014 05:01:02 -0600</pubDate>
  <link></link>
  <title><![CDATA[Senior Scientist (Agricultural Bio-informatics) (One post)]]></title>
  <description><![CDATA[
<p>Agricultural Scientists Recruitment Board</p>

<p>Qualifications Essential:<br />Doctoral degree in Bio-informatics/ Biotechnology/Molecular Biology and Biotechnology/Life Sciences/ Computer Sciences with specialization in Bio-informatics including relevant basic sciences with 8 years’ experience in the relevant subject as Scientist/Lecturer or in an equivalent position in the Pay Band- 3 of 15600-39100 with Grade Pay of 5400/6000/7000/8000 having made contribution to research/teachin/extension education as evidenced by published work/innovations and impact. </p>

<p>OR </p>

<p>Doctoral degree in the above subject(s) including relevant basic sciences with minimum 8 years’ experience of high quality post-doctoral research in an institution/organization as evidenced by at least 6 publications in journals with NAAS rating of 7.5 or above.</p>

<p>Desirable:<br />(i) Specialization and experience: Knowledge of software development and its application in crop bioinformatics, experience in handling ‘omies’data. <br />(ii) Teaching experience in relevant subject</p>

<p>The Secretary, Agricultural Scientists Recruitment Board, Indian Council of Agricultural Research Krishi Anusandhan Bhavan-I, Pusa New Delhi –110 012, India</p>

<p>Detailed eligibility criteria with how to apply information can be had at:<br />http://www.indiastudychannel.com/jobs/333467-Indian-Council-of-Agricultural-Research-looking-for-Assistant-Director-General.aspx</p>

<p>More at http://asrb.org.in/administrator/uploads_dir/1418978057english.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35762/genome-assembly-stats-plotting</guid>
	<pubDate>Wed, 28 Feb 2018 03:45:39 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35762/genome-assembly-stats-plotting</link>
	<title><![CDATA[Genome assembly stats plotting]]></title>
	<description><![CDATA[<p>A&nbsp;<em>de novo</em>&nbsp;genome assembly can be summarised b</p>
<p>y a number of metrics, including:</p>
<ul>
<li>Overall assembly length</li>
<li>Number of scaffolds/contigs</li>
<li>Length of longest scaffold/contig</li>
<li>Scaffold/contig N50 and N90Assembly base composition, in particular percentage GC and percentage Ns</li>
<li>CEGMA completeness</li>
<li>Scaffold/contig length/count distribution</li>
</ul>
<p>assembly-stats supports two widely used presentations of these values, tabular and cumulative length plots, and introduces an additional circular plot that summarises most commonly used assembly metrics in a single visualisation. Each of these presentations is generated using javascript from a common (JSON) data structure, allowing toggling between alternative views, and each can be applied to a single or multiple assemblies to allow direct comparison of alternate assemblies.</p>
<p>Tabular presentation allows direct comparison of exact values between assemblies, the limitations of this approach lie in the necessary omission of distributions and the challenge of interpreting ratios of values that may vary by several orders of magnitude.</p><p>Address of the bookmark: <a href="https://github.com/rjchallis/assembly-stats" rel="nofollow">https://github.com/rjchallis/assembly-stats</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/19820/rstudio</guid>
	<pubDate>Sat, 27 Dec 2014 06:50:58 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/19820/rstudio</link>
	<title><![CDATA[RStudio]]></title>
	<description><![CDATA[<p>RStudio IDE is a powerful and productive user interface for R. It&rsquo;s free and open source, and works great on Windows, Mac, and Linux.</p>
<p>The developers and expert trainers are the authors of several popular R packages, including ggplot2, plyr, lubridate, and others.</p>
<p>More at http://www.rstudio.com/</p>
<p>http://www.rstudio.com/products/RStudio/</p><p>Address of the bookmark: <a href="http://www.rstudio.com/" rel="nofollow">http://www.rstudio.com/</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36478/the-marvel-assembler</guid>
	<pubDate>Fri, 04 May 2018 19:18:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36478/the-marvel-assembler</link>
	<title><![CDATA[The MARVEL assembler]]></title>
	<description><![CDATA[<p><span>MARVEL consists of a set of tools that facilitate the overlapping, patching, correction and assembly of noisy (not so noisy ones as well) long reads.</span></p>
<p>The assembly process can be summarized as follows:</p>
<ol>
<li>overlap</li>
<li>patch reads</li>
<li>overlap (again)</li>
<li>scrubbing</li>
<li>assembly graph construction and touring</li>
<li>optional read correction</li>
<li>fasta file creation</li>
</ol><p>Address of the bookmark: <a href="https://github.com/schloi/MARVEL" rel="nofollow">https://github.com/schloi/MARVEL</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36597/gappadder-a-sensitive-approach-for-closing-gaps-on-draft-genomes-with-short-sequence-reads</guid>
	<pubDate>Mon, 14 May 2018 05:25:48 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36597/gappadder-a-sensitive-approach-for-closing-gaps-on-draft-genomes-with-short-sequence-reads</link>
	<title><![CDATA[GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads]]></title>
	<description><![CDATA[<p><span>This software is provided ``as is&rdquo; without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, including source codes, executables, and this documentation, is distributed free of charge. If you use this program in a publication, please cite the following reference:</span><br><span>Chong Chu, Xin Li, and Yufeng Wu. "GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads." bioRxiv (2017): 125534.</span></p><p>Address of the bookmark: <a href="https://github.com/Reedwarbler/GAPPadder" rel="nofollow">https://github.com/Reedwarbler/GAPPadder</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/20271/research-associate-tata-memorial-centre-advanced-centre-for-treatment-research-and-education-in-cancer-kharghar-navi-mumbai</guid>
  <pubDate>Thu, 08 Jan 2015 20:53:57 -0600</pubDate>
  <link></link>
  <title><![CDATA[Research Associate	@ TATA MEMORIAL CENTRE ADVANCED CENTRE FOR TREATMENT, RESEARCH AND EDUCATION IN CANCER KHARGHAR, NAVI MUMBAI]]></title>
  <description><![CDATA[
<p>TATA MEMORIAL CENTRE ADVANCED CENTRE FOR TREATMENT, RESEARCH AND EDUCATION IN CANCER KHARGHAR, NAVI MUMBAI – 410210</p>

<p>Website: www.actrec.gov.in; Ph: 27405000</p>

<p>No. ACTREC/Advt./ 66 /2014 23rd December, 2014<br />Research Associate	</p>

<p>International Cancer Genome Consortium (ICGC) - India Project (IRB Project No. 3 A/c. No. 2408)</p>

<p>Dr. Rajiv Sarin</p>

<p>Duration of the Project: One year Extendable up to Three years.</p>

<p>Consolidated Salary: Rs. 42,000/- p.m.</p>

<p>Application last date: 8th January, 2015.</p>

<p>Interview Date &amp; Time: 21st January, 2015, at 11.00 a.m.</p>

<p>Venue: Conference Room, 3rd floor, Khanolkar Shodhika, ACTREC.</p>

<p>Essential Qualifications and Experience:</p>

<p>Ph.D (any branch of Life Sciences)</p>

<p>The candidate must have at least one year experience after Ph.D., preferably in Genomics and Molecular Biology.</p>

<p>Candidates fulfilling these requirements should pre register themselves by sending their application in the prescribed format with recent CV and contact details of 2 referees by e-mail to icgc@actrec.gov.in latest 8th January, 2015 by 10.00 a.m.</p>

<p>Candidates shortlisted for the interview will be intimated by email on or before 9th January, 2015.</p>

<p>The interviews would be held on 21st January 2015 and will be only for the pre registered candidates who have been shortlisted.<br />No T.A./D.A. will be admissible for attending the interview.</p>

<p>At the time of Interview the candidate should bring original certificates along with CV with contact details of 2 referees and submit the photocopies (attested) of the certificates, with a recent passport size photograph.</p>

<p>Advertisement: www.actrec.gov.in/data%20files/2014/Walk-in-Research-Fellow-26-12-14.doc</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36997/cgview-circular-genome-viewer</guid>
	<pubDate>Wed, 20 Jun 2018 10:15:57 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36997/cgview-circular-genome-viewer</link>
	<title><![CDATA[CGView - Circular Genome Viewer]]></title>
	<description><![CDATA[CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature information and rendering options are supplied to the program using an XML file, a tab delimited file, or an NCBI ptt file. CGView converts the input into a graphical map (PNG, JPG, or Scalable Vector Graphics format), complete with labels, a title, legends, and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any web browser, allowing rapid genome browsing, and facilitating data sharing. The feature labels in maps can be hyperlinked to external resources, allowing CGView maps to be integrated with existing web site content or databases. For examples of the various output types, see the CGView gallery.

http://wishart.biology.ualberta.ca/cgview/gallery.html

http://stothard.afns.ualberta.ca/downloads/CCT/index.html

https://www.gview.ca/wiki/GView/WebHome

https://server.gview.ca/

http://stothard.afns.ualberta.ca/cgview_server/

Paper https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbx081/4037458<p>Address of the bookmark: <a href="http://wishart.biology.ualberta.ca/cgview/" rel="nofollow">http://wishart.biology.ualberta.ca/cgview/</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/20454/comparative-genomics-in-ensembl</guid>
	<pubDate>Wed, 21 Jan 2015 08:31:11 -0600</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/20454/comparative-genomics-in-ensembl</link>
	<title><![CDATA[Comparative Genomics in Ensembl]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/dDRdCnZOMCM" frameborder="0" allowfullscreen></iframe>The Ensembl browser provides viewable whole-genome alignments, homologues and phylogenetic gene trees, protein families, and ancestral sequences.  Learn how to view and export these data in this video.]]></description>
	
</item>

</channel>
</rss>