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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/27331?offset=940</link>
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	<description><![CDATA[]]></description>
	
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	<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>
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  <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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41689/medaka-sequence-correction-provided-by-ont-research</guid>
	<pubDate>Mon, 18 May 2020 16:28:00 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41689/medaka-sequence-correction-provided-by-ont-research</link>
	<title><![CDATA[medaka: Sequence correction provided by ONT Research]]></title>
	<description><![CDATA[<p><code>medaka</code><span>&nbsp;is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster.</span></p><p>Address of the bookmark: <a href="https://github.com/nanoporetech/medaka" rel="nofollow">https://github.com/nanoporetech/medaka</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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  <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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/44370/ncbiblast-2141-now-available</guid>
	<pubDate>Wed, 30 Aug 2023 02:36:13 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/44370/ncbiblast-2141-now-available</link>
	<title><![CDATA[NCBIBLAST+ 2.14.1 now available]]></title>
	<description><![CDATA[<p><a href="https://www.linkedin.com/feed/hashtag/?keywords=ncbiblast&amp;highlightedUpdateUrns=urn%3Ali%3Aactivity%3A7101231946264924160">#NCBIBLAST</a><span>+ 2.14.1 now available with improved documentation, faster and more reliable database downloads, and some bug fixes.&nbsp;</span></p><p>Check out the changes they made.</p><p>They added the&nbsp;<code><span>cleanup-blastdb-volumes.py</span></code>&nbsp;script to remove unused BLAST database volumes. Read the documentation&nbsp;<a href="https://www.ncbi.nlm.nih.gov/books/NBK592857/">here</a>.</p><p>They also switched the protocol from&nbsp;<code><span>ftp</span></code>&nbsp;to&nbsp;<code><span>https</span></code>&nbsp;to access BLAST databases for increased performance and reliability when downloading data from the NCBI with the&nbsp;<code><span>update_blastdb.pl</span></code>&nbsp;script.</p><p>And fixed a few bugs related to downloading data from the NCBI, and&nbsp;<code><span>mt_mode</span></code>&nbsp;crashing&nbsp;<code><span>blastn</span></code>&nbsp;and&nbsp;<code><span>blastx</span></code>.</p><p>Check out the&nbsp;<a href="https://www.ncbi.nlm.nih.gov/books/NBK131777/">release notes</a>.</p><p>Download&nbsp;<a href="https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.14.1/">BLAST+ 2.14.1</a></p><p>Questions or comments? Please write the&nbsp;<a href="https://support.nlm.nih.gov/support/create-case/">BLAST help desk</a>.</p><p><span><span>More info and download:</span>&nbsp;https://blast.ncbi.nlm.nih.gov/doc/blast-news/2023-BLAST-News.html</span></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
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	<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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/33955/crocoblast-optimized-parallel-implementation-of-local-sequence-alignment-algorithms</guid>
	<pubDate>Tue, 25 Jul 2017 05:03:10 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/33955/crocoblast-optimized-parallel-implementation-of-local-sequence-alignment-algorithms</link>
	<title><![CDATA[CrocoBLAST: Optimized parallel implementation of local sequence alignment algorithms]]></title>
	<description><![CDATA[<p><span>Local sequence alignment is a cornerstone of bioinformatics, allowing to compare the amino-acid sequences of different proteins, or the nucleotide sequences of different pieces of DNA. The Basic Local Alignment Search Tool (BLAST) has revolutionized the field of bioinformatics, and is currently implemented in all free and commercial bioinformatics packages. However, with the advent of Next Generation Sequencing (NGS) and the development of new sequencing techniques, the utility of traditional BLAST implementations is limited. CrocoBLAST combines the accuracy and general applicability of BLAST with computational efficiency, accessibility, and user experience, so that NGS data can be analyzed efficiently even when only modest computational resources are available.</span></p>
<p>https://webchem.ncbr.muni.cz/Platform/App/CrocoBLAST</p><p>Address of the bookmark: <a href="https://webchem.ncbr.muni.cz/Platform/App/CrocoBLAST" rel="nofollow">https://webchem.ncbr.muni.cz/Platform/App/CrocoBLAST</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34488/scripts-for-the-analysis-of-hgt-in-genome-sequence-data</guid>
	<pubDate>Wed, 29 Nov 2017 16:44:10 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34488/scripts-for-the-analysis-of-hgt-in-genome-sequence-data</link>
	<title><![CDATA[Scripts for the analysis of HGT in genome sequence data.]]></title>
	<description><![CDATA[<p><span>Scripts for the analysis of HGT in genome sequence data</span></p><p>Address of the bookmark: <a href="https://github.com/reubwn/hgt" rel="nofollow">https://github.com/reubwn/hgt</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/pages/view/36711/ancestral-sequence-reconstruction-steps</guid>
	<pubDate>Fri, 18 May 2018 08:28:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/36711/ancestral-sequence-reconstruction-steps</link>
	<title><![CDATA[Ancestral sequence reconstruction steps !]]></title>
	<description><![CDATA[<div><strong>Ancestral sequence reconstruction</strong>&nbsp;(<strong>ASR</strong>) &ndash; also known as&nbsp;<strong>ancestral gene</strong>/<strong>sequence reconstruction</strong>/<strong>resurrection</strong>&nbsp;&ndash; is a technique used in the study of&nbsp;molecular evolution. The method consists of the synthesis of an ancestral&nbsp;gene&nbsp;and expression of the corresponding ancestral&nbsp;protein.&nbsp;<a href="https://en.wikipedia.org/wiki/Ancestral_sequence_reconstruction#cite_note-thornton-1"></a>The idea of protein 'resurrection' was suggested in 1963 by Pauling and Zuckerkandl.<a href="https://en.wikipedia.org/wiki/Ancestral_sequence_reconstruction#cite_note-2"></a>&nbsp;Some early efforts were made in the eighties-nineties, led by the laboratory of&nbsp;Steven A. Benner, showing the potential of this technique &ndash; one that only started to be fulfilled in the post-genomic era.<a href="https://en.wikipedia.org/wiki/Ancestral_sequence_reconstruction#cite_note-3"></a>&nbsp;Thanks to the improvement of algorithms and of better sequencing and synthesis techniques, the method was developed further in the early 2000s to allow the resurrection of a greater variety of and much more ancient genes.<a href="https://en.wikipedia.org/wiki/Ancestral_sequence_reconstruction#cite_note-4"></a>&nbsp;Over the last decade, ancestral protein resurrection has developed as a strategy to reveal the mechanisms and dynamics of protein evolution.&nbsp;</div><div>&nbsp;</div><div>BEAST is the best way to predict the ancestral structure. but, I suggest following steps?</div><div>&nbsp;</div><div>1- Alignments "Mafft -&nbsp;<a href="https://www.researchgate.net/deref/http%3A%2F%2Fmafft.cbrc.jp%2Falignment%2Fsoftware%2Fsource.html" target="_blank">http://mafft.cbrc.jp/alignment/software/source.html</a>"</div><div>mafft --maxiterate 1000 --reorder --thread 24 --genafpair Dataset.fasta &gt; Dataset_Alig.fasta</div><div>&nbsp;</div><div>2- Your dataset has a good phylogenetic signal, is possible to perform with Tree-Puzzle "<a href="https://www.researchgate.net/deref/http%3A%2F%2Fwww.tree-puzzle.de" target="_blank">http://www.tree-puzzle.de</a>";</div><div>&nbsp;</div><div id="yui_3_14_1_1_1526649596608_1443">3 - This dataset which the saturation index, I perform with "<a href="https://www.researchgate.net/deref/http%3A%2F%2Fdambe.bio.uottawa.ca%2Fdambe.asp" target="_blank">http://dambe.bio.uottawa.ca/dambe.asp</a>";</div><div>&nbsp;</div><div>4- Has evidence of possible recombination in your dataset, the evaluate if this presence or absence, because this may to influence the grouping of clades, I perform with</div><div>---recombination</div><div>&nbsp;</div><div>4.1- Phi-test, implemented in SplitTree4"<a href="https://www.researchgate.net/deref/http%3A%2F%2Fwww.splitstree.org" target="_blank">http://www.splitstree.org</a>", (.nex file)</div><div>&nbsp;</div><div>4.2- GARD deployed in webserver in the DataMonkey "<a href="https://www.researchgate.net/deref/http%3A%2F%2Fwww.datamonkey.org%2F" target="_blank">http://www.datamonkey.org/</a>" - turning to the amino acid seaview -&gt; view proteins -&gt; save as ...) Ideally do a tree-based groups.</div><div>&nbsp;</div><div>4.3- RDP4 for download and installation on Windows in "<a href="https://www.researchgate.net/deref/http%3A%2F%2Fweb.cbio.uct.ac.za%2F~darren%2Frdp.html" target="_blank">http://web.cbio.uct.ac.za/~darren/rdp.html</a>"</div><div>&nbsp;</div><div>4.4- Hyphy (Mac, Windows, Linux) in "<a href="https://www.researchgate.net/deref/http%3A%2F%2Fhyphy.org%2Fw%2Findex.php%2FDownload" target="_blank">http://hyphy.org/w/index.php/Download</a>"</div><div>&nbsp;</div><div>4.5- Path-o-Gen (temporal structure of a tree input file -&gt; arquivo.tre)</div><div>These steps above, I call of pre-processing to inferences phylogenetic...</div><div>&nbsp;</div><div>5- Perform phylogenetic tree, used Bayesian Inference with Molecular Clock, but is necessary Clock Testing:</div><div>&nbsp;</div><div>- This step is performed with program Beast (Beauti, Beast and TreeAnnotator), and Tracer_v1.5 more FigTree to inspection.</div><div>&nbsp;</div><div>- Tutorials:&nbsp;<a href="https://www.researchgate.net/deref/http%3A%2F%2Fbeast.bio.ed.ac.uk%2Ftutorials" target="_blank">http://beast.bio.ed.ac.uk/tutorials</a></div><div>- Downloads:&nbsp;<a href="https://www.researchgate.net/deref/http%3A%2F%2Fbeast.bio.ed.ac.uk%2Fdownloads" target="_blank">http://beast.bio.ed.ac.uk/downloads</a></div>]]></description>
	<dc:creator>Surabhi Chaudhary</dc:creator>
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