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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/30104?offset=850</link>
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	<description><![CDATA[]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41896/kad-assessing-genome-assemblies-using-k-mer-copies-in-assemblies-and-k-mer-abundance-in-illumina-reads</guid>
	<pubDate>Fri, 19 Jun 2020 07:34:12 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41896/kad-assessing-genome-assemblies-using-k-mer-copies-in-assemblies-and-k-mer-abundance-in-illumina-reads</link>
	<title><![CDATA[KAD: Assessing genome assemblies using K-mer copies in assemblies and K-mer abundance in Illumina reads]]></title>
	<description><![CDATA[<p>KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies. Briefly, abundance of k-mers are quantified for both sequencing reads and assembly sequences. Comparison of the two values results in a single value per k-mer, K-mer Abundance Difference (KAD), which indicates how well the assembly matches read data for each k-mer.</p>
<p><a href="https://render.githubusercontent.com/render/math?math=KAD=log_{2}\begin{pmatrix}\frac{c%2Bm}{m(n%2B1)}\end{pmatrix}" target="_blank"><img src="https://render.githubusercontent.com/render/math?math=KAD=log_{2}\begin{pmatrix}\frac{c%2Bm}{m(n%2B1)}\end{pmatrix}" alt="image" style="border: 0px;"></a></p>
<p>where,&nbsp;<em>c</em>&nbsp;is the count of a k-mer from reads,&nbsp;<em>m</em>&nbsp;is the mode of counts of read k-mers, and&nbsp;<em>n</em>&nbsp;is the copy of the k-mer in the assembly.</p><p>Address of the bookmark: <a href="https://github.com/liu3zhenlab/KAD" rel="nofollow">https://github.com/liu3zhenlab/KAD</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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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/43112/calling-variants-in-non-diploid-systems</guid>
	<pubDate>Sat, 26 Jun 2021 15:37:49 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43112/calling-variants-in-non-diploid-systems</link>
	<title><![CDATA[Calling variants in non-diploid systems]]></title>
	<description><![CDATA[<p><span>The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been accomplished on human mitochondrial&nbsp;</span><span>DNA</span><span>&nbsp;although the same approaches will work equally good on viral and bacterial genomes (</span><a href="https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html#Rebolledo-Jaramillo2014">Rebolledo-Jaramillo&nbsp;<em>et al.</em>&nbsp;2014</a><span>,&nbsp;</span><a href="https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html#Li2015">Li&nbsp;<em>et al.</em>&nbsp;2015</a><span>).</span></p><p>Address of the bookmark: <a href="https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html" rel="nofollow">https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19544/sau-bioinformaticsplant-biotech-jrf-vacancy</guid>
  <pubDate>Fri, 12 Dec 2014 21:27:12 -0600</pubDate>
  <link></link>
  <title><![CDATA[SAU Bioinformatics/Plant Biotech JRF Vacancy]]></title>
  <description><![CDATA[
<p>Applications are invited for the post of Junior Research Fellow (JRF) to work on SERB, DST funded project entitled “Genome wide analysis of ascorbate oxidase multi-gene family and elucidating its role in negative regulation of stress response in rice” under the supervision of Dr. Ananda Mustafiz, Faculty of Life Sciences and Biotechnology, South Asian University.</p>

<p>Qualification: Highly motivated M.Sc. (Bioinformatics/ Biotechnology/ Life Sciences/ Botany/ Agriculture) students are encouraged to apply. Prior experience in Bioinformatics/Plant tissue culture work is preferable. Preferences would be given to DBT/ CSIR / UGC NET qualified students.</p>

<p>Application Procedure: A detailed CV indicating name, date of birth, address, contact number, e-mail address, educational qualifications, NET qualified or not, research experiences if any, should be e-mailed to This email address is being protected from spambots. You need JavaScript enabled to view it. on or before 24th December 2014.</p>

<p>Important Note: Only short listed candidates will be called for interview at Akbar Bhawan, Chanakyapuri, New Delhi. No TA/DA will be paid for attending the interview. SAU Selection Committee reserves the rights to relax any of the qualifications in case the candidate is found otherwise well qualified. The above- mentioned post is temporary and will be initially offered for a period of one year, which can be extended to one more year.</p>

<p>Advertisement:  www.sau.ac.in/recruitment/vacancy.html</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43766/genometools-the-versatile-open-source-genome-analysis-software</guid>
	<pubDate>Wed, 02 Feb 2022 04:00:21 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43766/genometools-the-versatile-open-source-genome-analysis-software</link>
	<title><![CDATA[GenomeTools: The versatile open source genome analysis software]]></title>
	<description><![CDATA[<p>The&nbsp;<em>GenomeTools</em>&nbsp;genome analysis system is a&nbsp;<a href="http://genometools.org/license.html">free</a>&nbsp;collection of bioinformatics&nbsp;<a href="http://genometools.org/tools.html">tools</a>&nbsp;(in the realm of genome informatics) combined into a single binary named&nbsp;<em>gt</em>. It is based on a C library named &ldquo;libgenometools&rdquo; which consists of several modules.</p>
<p><img src="http://genometools.org/images/annotation.png" alt="image" style="border: 0px;"></p>
<p>If you are interested in gene prediction, have a look at&nbsp;<a href="http://genomethreader.org/" title="GenomeThreader gene prediction        software"><em>GenomeThreader</em></a>.</p>
<p>http://genometools.org/pub/</p><p>Address of the bookmark: <a href="http://genometools.org/" rel="nofollow">http://genometools.org/</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19635/walk-in-interview-for-research-associate-studentship-and-traineeship-at-bif-nehu-tura-campus</guid>
  <pubDate>Thu, 18 Dec 2014 11:02:05 -0600</pubDate>
  <link></link>
  <title><![CDATA[Walk in interview for Research Associate, Studentship and Traineeship at BIF, NEHU, Tura Campus]]></title>
  <description><![CDATA[
<p>BIOINFORMATICS INFRASTRUCTURE FACILITY (BIF)<br />Department of RDAP<br />North-Eastern Hil University, Tura Campus<br />Tura-79402, Meghalaya</p>

<p>Walk in interview for Research Associate, Studentship and Traineeship at BIF</p>

<p>Applications are invited for the Post of Research Associate, Traineeship and Studentship in the DBT sponsored Bioinformatics Infrastructure Facility (BIF) at the Bioinformatics Centre, Department of RDAP, North-Eastern Hil University, Tura Campus, Tura-79402, Meghalaya. The Posts are purely temporary and terminable at any time without prior notice or assigning any reason thereof. The person engaged, shall not be entailed for any claim implicit or explicit for permanent absorption in the University.</p>

<p>Research Associate- 01</p>

<p>Essential Qualification: M.Sc. in Bioinformatics/Biotechnology from a recognized University/ institute.</p>

<p>Desirable: PhD or Pursuing PhD in the relevant subject(s) or equivalent published work in reputed peer reviewed journals or Advance PG diploma in Bioinformatics courses.</p>

<p>Duties: Creation of database, web designing, maintenance of internet, training of students in Bioinformatics, handling and knowledge of Bioinformatics software tools and technique, conducting Bioinformatics based research and other day to day laboratory work, writing report and scientific papers.</p>

<p>Pay:Rs. 2,00/- + Admissible 10% HRA per month</p>

<p>Age: Below 35 years</p>

<p>Traineeship- 02</p>

<p>Students who have completed Masters Degree in Bioinformatics/Biotechnology or any branch of Life Sciences/Agricultural Sciences/Computer Science to cary out a project work in Bioinformatics.</p>

<p>Desirable: Prior Knowledge of programming languages such as C, JAVA, MySQL is preferable.</p>

<p>Stipend: Rs. 800/- p.m. fixed. Purely temporary for a period of six months.</p>

<p>Studentship: 02</p>

<p>Students pursuing postgraduate degree in Bioinformatics/biotechnology/Agricultural Sciences or any branch of Life Science</p>

<p>Desirable: Prior knowledge of bioinformatics/ programming language is preferable.</p>

<p>Stipend: 800/- p.m. fixed. Purely temporary for a period of six months.</p>

<p>Candidates must send the detailed Biodata via mail/post and bring al the relevant documents in original and one set of attested photocopies of the same at the time of interview. No TA/DA will be paid for attending the interview and candidates have to make their own arrangements.</p>

<p>Last date for receiving application by mail or by post: 16.02.2014</p>

<p>Contact Information:<br />Dr.B.K. Mishra<br />Cordinator BIF,<br />RDAP Department, NEHU, Tura Campus<br />Phone: 91-03651-23107<br />Fax: 91-03651-23953<br />E-mail: drbkm1972@yaho.co.in, birendramishra14@gmail.com</p>

<p>Advertisement: http://www.nehu.ac.in/Advertisements/BIF_TuraAdtvPV_171214.pdf</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>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19597/assistant-professor-at-gauhati-university-guwahati</guid>
  <pubDate>Tue, 16 Dec 2014 01:15:30 -0600</pubDate>
  <link></link>
  <title><![CDATA[Assistant Professor at GAUHATI UNIVERSITY, GUWAHATI]]></title>
  <description><![CDATA[
<p>Advt. No.T/2014/4</p>

<p>Ref. No. GU/Estt/T/308(VI)/2014/6451-61</p>

<p>Applications are invited from the Indian citizens for five (5) teaching posts of Assistant Professor (Contractual) under various departments of Gauhati University. Details of the advertisement, other terms and conditions and the application forms are available in the University website www.gauhati.ac.in</p>

<p>Asstt. Professor (Contractual)</p>

<p>    2. M.Sc. Microbiology Course in Botany</p>

<p>    3 1.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biochemistry (1 post). (Preference will be given to candidates having experience in Biochemistry).</p>

<p>    2.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biotechnology(1 post). (Preference will be given to candidates having experience in Bioinformatics).</p>

<p>    3.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc.  Biotechnology(1 post). (Preference will be given to candidates having experience in Microbial Genetics).</p>

<p>As per UGC norms</p>

<p>Pay Band &amp; Academic Grade Pay : (Consolidated pay) : Rs. 21,600/- per month</p>

<p>Application Form : Prescribe application form may download from the G.U. website www.gauhati.ac.in</p>

<p>Last date of receipt of filled-in application is 08.01.2015.</p>

<p>Advertisement: www.gauhati.ac.in/openfile.php?file=Notice1258.pdf</p>
]]></description>
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<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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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19695/china-university-of-macau-phd-position-2015-in-bioinformatics-computer-science</guid>
  <pubDate>Mon, 22 Dec 2014 00:12:49 -0600</pubDate>
  <link></link>
  <title><![CDATA[China University of Macau PhD Position 2015 in Bioinformatics, Computer Science]]></title>
  <description><![CDATA[
<p>The Computational Biology and Bioinformatics Group at the University of Macau is inviting applications for PhD Position. Applicants will work on a research project focusing on the flexible receptor protein-ligand docking algorithms for computer-aided drug design.  The candidate will be working as part of a team in developing novel metaheuristic algorithms and scoring functions for large-scale, highly flexible protein-ligand docking problems. The duration of this PhD position is 2-3 years, starting in August 2015. Remuneration paid to candidate is MOP 11000-14000/month (~USD 1375-1750/month). The applications should be submitted before March 2015.</p>

<p>Study Subject(s): PhD position is award in the field of Bioinformatics/Computer Science.<br />Course Level: Position is available for pursuing PhD degree level at the University of Macau.<br />Scholarship Provider: University of Macau<br />Scholarship can be taken at: China</p>

<p>Eligibility: The ideal candidate would be a master degree holder in Bioinformatics or related disciplines with knowledge in Medical sciences or Life sciences (with GPA of at least 3.0 on a 4-point scale or equivalent) . Knowledge in programming (C and C++) and Linux scripting are necessary; experience in molecular docking, molecular dynamics simulations or molecular modeling is an advantage. The candidate should be fluent in spoken and written English; preference will be given to applicants with good publication records in relevant areas.</p>

<p>Scholarship Open for International Students: Researchers from China can apply for this PhD position.</p>

<p>Scholarship Description:</p>

<p>The Computational Biology and Bioinformatics Group at the University of Macau is looking for a motivated PhD student in Bioinformatics or Computer Science to work on a research project focusing on the flexible receptor protein-ligand docking algorithms for computer-aided drug design.  The candidate will be working as part of a team in developing novel metaheuristic algorithms and scoring functions for large-scale, highly flexible protein-ligand docking problems.</p>

<p>Number of award(s): There is only one PhD position available.</p>

<p>Duration of award(s): The duration of this PhD position is 2-3 years.</p>

<p>What does it cover? Remuneration paid to candidate is  MOP 11000-14000/month (~USD 1375-1750/month).</p>

<p>Selection Criteria: Not Known</p>

<p>Notification: Not Known</p>

<p>How to Apply: Send your current CV, your academic transcripts, a letter of motivation and research interests, two letters of recommendations from academic faculty to Dr. Shirley Siu at shirleysiu[at]umac.mo before March 2015.</p>

<p>Scholarship Application Deadline: The applications should be submitted before March 2015.</p>
]]></description>
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