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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/19980?offset=730</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42160/vicuna-a-software-tool-that-enables-consensus-assembly-of-ultra-deep-sequence-derived-from-diverse-viral-or-other-heterogeneous-populations</guid>
	<pubDate>Tue, 25 Aug 2020 03:40:17 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42160/vicuna-a-software-tool-that-enables-consensus-assembly-of-ultra-deep-sequence-derived-from-diverse-viral-or-other-heterogeneous-populations</link>
	<title><![CDATA[VICUNA: a software tool that enables consensus assembly of ultra-deep sequence derived from diverse viral or other heterogeneous populations.]]></title>
	<description><![CDATA[<p><span>VICUNA</span><span>&nbsp;is a&nbsp;</span><em>de novo</em><span>&nbsp;assembly program targeting populations with high mutation rates. It creates a single linear representation of the mixed population on which intra-host variants can be mapped. For clinical samples rich in contamination (e.g., &gt;95%), VICUNA can leverage existing genomes, if available, to assemble only target-alike reads. After initial assembly, it can also use existing genomes to perform guided merging of contigs. For each data set (e.g., Illumina paired read, 454), VICUNA outputs consensus sequence(s) and the corresponding multiple sequence alignment of constituent reads. VICUNA efficiently handles ultra-deep sequence data with tens of thousands fold coverage.</span></p>
<p><a href="http://software.broadinstitute.org/viral/docs/vicuna_v1.0.pdf">http://software.broadinstitute.org/viral/docs/vicuna_v1.0.pdf</a></p><p>Address of the bookmark: <a href="https://www.broadinstitute.org/viral-genomics/vicuna" rel="nofollow">https://www.broadinstitute.org/viral-genomics/vicuna</a></p>]]></description>
	<dc:creator>biogeek</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43439/mmseqs2-ultra-fast-and-sensitive-sequence-search-and-clustering-suite</guid>
	<pubDate>Wed, 06 Oct 2021 07:01:14 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43439/mmseqs2-ultra-fast-and-sensitive-sequence-search-and-clustering-suite</link>
	<title><![CDATA[MMseqs2: ultra fast and sensitive sequence search and clustering suite]]></title>
	<description><![CDATA[<p><span>MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.</span></p><p>Address of the bookmark: <a href="https://github.com/soedinglab/MMseqs2" rel="nofollow">https://github.com/soedinglab/MMseqs2</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44904/termal-a-fast-and-interactive-terminal-based-viewer-for-multiple-sequence-alignments</guid>
	<pubDate>Mon, 22 Sep 2025 23:51:02 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44904/termal-a-fast-and-interactive-terminal-based-viewer-for-multiple-sequence-alignments</link>
	<title><![CDATA[Termal: a fast and interactive terminal-based viewer for multiple sequence alignments]]></title>
	<description><![CDATA[<p>termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC) clusters.</p>
<p>https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbaf208/8257678?login=true</p><p>Address of the bookmark: <a href="https://github.com/sib-swiss/termal" rel="nofollow">https://github.com/sib-swiss/termal</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42713/gggenomes-a-grammar-of-graphics-for-comparative-genomics</guid>
	<pubDate>Mon, 01 Feb 2021 14:47:32 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42713/gggenomes-a-grammar-of-graphics-for-comparative-genomics</link>
	<title><![CDATA[gggenomes: A grammar of graphics for comparative genomics]]></title>
	<description><![CDATA[<p><span>gggenomes is a versatile graphics package for comparative genomics. It extends the popular R visualization package</span><a href="https://ggplot2.tidyverse.org/">ggplot2</a><span>&nbsp;by adding dedicated plot functions for genes, syntenic regions, etc. and verbs to manipulate the plot to, for example, quickly zoom in into gene neighborhoods.</span></p><p>Address of the bookmark: <a href="https://github.com/thackl/gggenomes" rel="nofollow">https://github.com/thackl/gggenomes</a></p>]]></description>
	<dc:creator>Surabhi Chaudhary</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/24462/icar-project-ra-position-institute-of-bioinformatics-iob-bangalore</guid>
  <pubDate>Tue, 22 Sep 2015 23:41:31 -0500</pubDate>
  <link></link>
  <title><![CDATA[ICAR project RA position @ Institute of Bioinformatics (IOB) Bangalore]]></title>
  <description><![CDATA[
<p>Applications are invited for the post of Research Associate (RA) in the ICAR project on "Lactation stress associated postpartum anestrus SNP array in buffaloes". We are looking for a motivated candidate for handling Next Generation sequencing data analysis with a strong background in bioinformatics and programming.</p>

<p>The position is open for immediate appointment and available for two years and then extendable for additional one year. The applicant will be appointed as Research Associate based on qualifications as detailed below:</p>

<p>Research Associate:</p>

<p>-Master’s degree with bioinformatics with at least 2 years of research experience in Next Generation sequencing data analysis as evidence from Fellowship/ Associateship / Training / other engagements.</p>

<p>-Familiarity with bioinformatics tools, database development, programming skills</p>

<p>-Minimum 1 publication in any peer reviewed journal</p>

<p>Salary will be as per ICAR rules and guidelines. Application will be shortlisted based on CV, reference letters from mentors and telephonic interview. Candidates will be called for a personal interview at Bangalore before appointment. No travel expense will be provided for attending interview at Bangalore.</p>

<p>Interested candidates may send a Letter of Interest and CV by email to: keshav@ibioinformatics.org before September 29, 2015.</p>
]]></description>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/24463/project-fellow-at-indian-institute-of-chemical-biology-iicb</guid>
  <pubDate>Tue, 22 Sep 2015 23:47:35 -0500</pubDate>
  <link></link>
  <title><![CDATA[Project Fellow at Indian Institute of Chemical Biology (IICB)]]></title>
  <description><![CDATA[
<p>Advertisement No. : R&amp;C/CD/427/2015  ,Vacancy Code: 4271501    </p>

<p>Project Fellow Bioinformatics recruitment in Indian Institute of Chemical Biology (IICB) purely temporary </p>

<p>Name of the Project:  "Genomics and Informatics Solutions for Integrating Biology(Genesis)".     </p>

<p>No. of Vacancies: 1     </p>

<p>Qualification required : M.Sc in Bioinformatics with 55% Marks. </p>

<p>Experience (Desirable): Candidate should be well versed with sequencing data analysis,assembly and annotation of whole genome sequence. Experience in transcriptional data analysis is also preferred.</p>

<p>Age Limit : 28 Years   <br />  <br />Stipend : Rs.16000<br />How to apply<br />Interested candidates may appear for the walk-in-interview to be held on 28.09.2015 from 11.00 a.m. in the Red Carpet Room with the following documents self attested copy - (1) Matriculation Certificate in support of your date of birth, (2) Degree/Diploma Certificate, (3) Original reprints of all testimonials regarding educational qualification, (4) No Objection Certificate from the employer if employed, (5) Final Mark Sheet of M.Sc. Examination, (6) One Passport size photograph.</p>

<p>http://www.career.iicb.res.in/Recruitment%20Notice.php</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/26587/last</guid>
	<pubDate>Wed, 09 Mar 2016 14:27:01 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26587/last</link>
	<title><![CDATA[LAST]]></title>
	<description><![CDATA[<p style="text-align: center;"><img src="http://last.cbrc.jp/lastwebfig.png" alt="sketch of  similar regions in sequences" style="border: 0px;"></p>
<p>LAST can:</p>
<ul>
<li>Handle <strong>big</strong> sequence data, e.g:
<ul>
<li>Compare two vertebrate genomes</li>
<li>Align billions of DNA reads to a genome</li>
</ul>
</li>
<li>Indicate the <a href="http://lastweb.cbrc.jp/about.html">reliability</a> of each aligned column.</li>
<li>Use sequence quality data <a href="http://nar.oxfordjournals.org/content/38/7/e100.abstract">properly</a>.</li>
<li>Compare DNA to proteins, with frameshifts.</li>
<li>Compare PSSMs to sequences</li>
<li>Calculate the likelihood of chance similarities between random sequences.</li>
<li>Do split and spliced alignment.</li>
<li><a href="http://last.cbrc.jp/doc/last-train.html">Train</a> alignment parameters for unusual kinds of sequence (e.g. nanopore).</li>
</ul><p>Address of the bookmark: <a href="http://last.cbrc.jp/" rel="nofollow">http://last.cbrc.jp/</a></p>]]></description>
	<dc:creator>Archana Malhotra</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/25770/fellowship-doctoral-research-in-biomedical-genomics-including-statistical-genomics</guid>
  <pubDate>Sun, 20 Dec 2015 06:03:43 -0600</pubDate>
  <link></link>
  <title><![CDATA[Fellowship (Doctoral Research In Biomedical Genomics, Including Statistical Genomics)]]></title>
  <description><![CDATA[
<p>Fellowship (Doctoral Research In Biomedical Genomics, Including Statistical Genomics)<br />Eligibility : MSc(Bio-Chemistry, Bio-Informatics, Bio-Tech, Mathematics / Applied Mathematics, Stati, Zoology)<br />Location : Kolkata<br />Last Date : 31 Dec 2015<br />Hiring Process : Written-test</p>

<p>NO: 340/ESTB/ADMN/NIBMG/2015-16 <br />Doctoral Research In Biomedical Genomics, Including Statistical Genomics conduct National Institute of Biomedical Genomics (NIBMG)<br />Information For Students Interested To Pursue Doctoral Research In Biomedical Genomics, Including Statistical Genomics, At The National Institute Of Biomedical Genomics (Nibmg), Kalyan<br />Eligibility conditions for specific areas of research are :<br />Statistical Genomics : An applicant who wishes to pursue research in Statistical Genomics should hold a Master's degree (First class or equivalent) in a relevant discipline (Statistics, Mathematics, Bioinformatics, or a related discipline)<br />Biomedical Genomics : An applicant who wishes to pursue research in any area of biomedical genomics, other than statistical genomics, should hold a Master's degree (First class or equivalent) in a relevant discipline (Biochemistry, Biotechnology, Molecular Biology, Genetics, Zoology, Physiology, or a related discipline)<br />Fellowship : An applicant should have passed the NET conducted by CSIR/UGC/ICMR/DBT within the past ONE year AND should have been awarded a valid Junior Research Fellowship from CSIR, UGC, ICMR, DBT (Category-I only), DST (INSPIRE), NBHM. Preference will be given to candidates with demonstrable research training in the form of summer training or short-term courses in established research laboratories in preparation for a research career in biomedical sciences<br />How to apply<br />Online application will be accepted until 5 PM of December 31, 2015. A formal interview of the short-listed candidates will be held on January 12, 2016</p>

<p>More at http://www.nibmg.ac.in/?q=Career%20Opportunities</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/26568/research-scientist-at-iit-madras</guid>
  <pubDate>Mon, 07 Mar 2016 04:06:13 -0600</pubDate>
  <link></link>
  <title><![CDATA[Research Scientist at IIT Madras]]></title>
  <description><![CDATA[
<p>Research Scientist/Project Associate/Project Assistant Jobs opportunity in Indian Institute of Technology Madras (IIT Madras)</p>

<p>Research Scientist</p>

<p>Qualification : Ph.D in any branch of life science or bioinformatics or computational biology Experience : Previous experience in Molecular Biology, Cell Biology, Biochemistry and Genome/big data analysis is desirable but not mandatory</p>

<p>No. of Vacancy : 02</p>

<p>Project Associate</p>

<p>Qualification : MSc in any branch of life science Experience Previous experience in Molecular Biology, Cell Biology and Biochemistry is desirable but not mandatory</p>

<p>No. of Vacancy : 02</p>

<p>Project Assistant</p>

<p>Qualification : BSc in any branch of life science or chemical science Experience Previous experience any branch in Life science, Molecular Biology, Cell Biology and Biochemistry is desirable but not mandatory</p>

<p>No. of Vacancy : 03<br />How to apply</p>

<p>Interested candidates can forward their profiles to email id: nctb@iitm.ac.in latest by 18th March, 2016</p>

<p>More at https://www.iitm.ac.in/content/national-cancer-tissue-bio-bank-department-biotechnology-iitm-chennai-vacancy-various-post<br />https://www.iitm.ac.in/sites/default/files/notices/vacancy.pdf</p>
]]></description>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/26335/ra-at-central-university-of-rajasthan</guid>
  <pubDate>Tue, 09 Feb 2016 03:53:35 -0600</pubDate>
  <link></link>
  <title><![CDATA[RA at Central University of Rajasthan]]></title>
  <description><![CDATA[
<p>Research Fellow Bioinformatics</p>

<p>Eligibility : MSc(Bio-Chemistry, Bio-Informatics, Bio-Tech)</p>

<p>Location : Ajmer</p>

<p>Last Date : 13 Feb 2016</p>

<p>Hiring Process : Face to Face Interview<br />Central University of Rajasthan</p>

<p>Research Fellow Job vacancies in Central University of Rajasthan</p>

<p>Project Title : “Development of natural product derived febrifugine ananlogues as a novel therapeutics against visceral leishmaniasis”</p>

<p>No. of Post : 01</p>

<p>Qualification : Master of Biochemistry, Biotechnology, Bioinformatics and related biological sciences with minimum 55%, Age limit as per government rule.</p>

<p>Desirable Experience : Candidates with experience in cell culture, Chemoinformatics, and Parasitology will be preferred.    </p>

<p>Fellowship : Rs. 25,000/- p.m. consolidated for NET qualified (14,000/- p.m. consolidated for Non-NET)<br />How to apply</p>

<p>The candidates may apply on a plain paper, along with their curriculum vitae (including name, date of birth, academic qualification starting from 10th class, summary of research experience, email id, phone number and passport size photograph) and email to vkprajapati@curaj.ac.in or post the hard copy to the Dr. Vijay Kumar Prajapati PI, DST-SERB Project (YSS/2015/000716), Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Dist- Ajmer, Rajasthan, 305 817 on or before 13th February 2016.</p>

<p>More at http://www.curaj.ac.in/Default.aspx?PageId=241</p>
]]></description>
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