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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/28903?offset=1020</link>
	<atom:link href="https://bioinformaticsonline.com/related/28903?offset=1020" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19248/bioinformatics-jrfrasrf-position-at-institute-of-cytology-and-preventive-oncology-icpo</guid>
  <pubDate>Wed, 19 Nov 2014 20:16:32 -0600</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics JRF/RA/SRF position at Institute of Cytology and Preventive Oncology (ICPO)]]></title>
  <description><![CDATA[
<p>Institute of Cytology and Preventive Oncology (ICPO) I-7, Sector-39, Noida-201301</p>

<p>Candidates having the below mentioned qualifications may appear for walk in interview at ICPO on 2nd December 2014 between 10.00 AM and 12:00 PM under the below time bound projects under Dr. Subhash M. Agarwal, Scientist C. The post is purely temporary and co-terminus with the project.</p>

<p>Research Assistant (One)<br />25650/- consolidated<br />Discovery of EGFR secondary mutant inhibitors using structure based screening approach (ICMR)<br />Duration: 7 months</p>

<p>Essential: M.Sc./ M.Tech in Bioinformatics or any other related subject with good academic record.</p>

<p>Desirable: Experience in scripting and molecular docking.<br />	<br />Below 30 years</p>

<p>Junior Research Fellow (One)</p>

<p>16,000 + 30% HRA = Rs. 20800/-</p>

<p>Identification of novel inhibitors targeting EGFR using an integrated ligand and structure based approach (DBT)</p>

<p>Duration: 9 months</p>

<p>Essential: M.Sc./ M.Tech in Bioinformatics or any other related subject with good academic record. Candidates with CSIR-UGC / ICMR, NET qualification will be preferred</p>

<p>Desirable: Experience in scripting, QSAR and molecular docking.<br />	<br />Below 28 years</p>

<p>Interested eligible candidates may send their applications with Bio-data by email at (smagarwal@gmail.com) or by post addressed to Dr. Subhash M Agarwal, Scientist C, Institute of Cytology and Preventive Oncology (ICPO) I-7, Sector-39, Noida-201301 so as to reach latest by 1st December, 2014. The candidates may appear for interview at ICPO along with 3 copies of CV, photo and relevant certificates of qualifications in original and reprints of publications at the time of interview. It should be noted that No TA/DA will be paid for the walk in Interview.</p>

<p>Advertisement: www.icpo.org.in/advt-walk-in-interview.docx</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43658/uniquekmer-generate-unique-kmers-for-every-contig-in-a-fasta-file</guid>
	<pubDate>Fri, 17 Dec 2021 00:08:15 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43658/uniquekmer-generate-unique-kmers-for-every-contig-in-a-fasta-file</link>
	<title><![CDATA[UniqueKmer: Generate unique KMERs for every contig in a FASTA file]]></title>
	<description><![CDATA[<p dir="auto">Generate unique k-mers for every contig in a FASTA file.</p>
<p dir="auto">Unique k-mer is consisted of k-mer keys (i.e. ATCGATCCTTAAGG) that are only presented in one contig, but not presented in any other contigs (for both forward and reverse strands).</p>
<p dir="auto">This tool accepts the input of a FASTA file consisting of many contigs, and extract unique k-mers for each contig.</p>
<p dir="auto">The output unique k-mer file and Genome file can be used for fastv:&nbsp;<a href="https://github.com/OpenGene/fastv">https://github.com/OpenGene/fastv</a>, which is an ultra-fast tool to identify and visualize microbial sequences from sequencing data.</p>
<p>https://github.com/OpenGene/UniqueKMER</p><p>Address of the bookmark: <a href="https://github.com/OpenGene/UniqueKMER" rel="nofollow">https://github.com/OpenGene/UniqueKMER</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/19556/genome-origami</guid>
	<pubDate>Fri, 12 Dec 2014 22:48:17 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/19556/genome-origami</link>
	<title><![CDATA[Genome Origami]]></title>
	<description><![CDATA[<p>There are several interesting factoid about our genomes, one of them is their folding. If we stretched out the DNA in a single cell, which is only a few millionths of an inch wide, it would span more than six feet. In other word, the size of six feet DNA fold themself to fit in a few millionths of an inch wide space. These DNA folding is a dynamic process that changes over time (!!). Researchers around the world have been trying to understand how DNA folds itself up so efficiently, and a recent post on the NIH Director&rsquo;s Blog highlights new research illustrating how the human genome folds inside the cell&rsquo;s nucleus, as well as how DNA folding affects gene regulation. The research team created this delightful video that demonstrates the principles involved using origami art.</p><p>http://bioinformaticsonline.com/videolist/watch/19555/a-3d-map-of-the-human-genome<br /><br />Researchers have been working to determine how cells regulate gene expression for nearly as long as we&rsquo;ve known about DNA. How, for example, do nerve cells know to turn off only nerve cell genes and turn off bone cell genes? DNA folding loops are part of the answer. This research team, which published their findings in a paper in Cell http://www.cell.com/cell/abstract/S0092-8674%2814%2901497-4 , found that the number of loops is much lower than expected. There are only 10,000 loops instead of the predicted millions, and they form on/off switches in DNA.<br /><br /></p><p>More at http://www.eurekalert.org/pub_releases/2014-12/ru-3mr121114.php</p><p>Reference http://www.cell.com/cell/abstract/S0092-8674%2814%2901497-4</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43799/kast</guid>
	<pubDate>Wed, 23 Feb 2022 08:28:36 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43799/kast</link>
	<title><![CDATA[KAST]]></title>
	<description><![CDATA[<p><span>Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.</span></p><p>Address of the bookmark: <a href="https://github.com/martinjvickers/KAST" rel="nofollow">https://github.com/martinjvickers/KAST</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/19545/walk-%E2%80%93-in-%E2%80%93-interview-agricultural-knowledge-management-unit-indian-agricultural-research-institute-new-delhi-110012</guid>
  <pubDate>Fri, 12 Dec 2014 21:33:02 -0600</pubDate>
  <link></link>
  <title><![CDATA[WALK – IN – INTERVIEW @ Agricultural Knowledge Management Unit Indian Agricultural Research Institute, New Delhi-110012]]></title>
  <description><![CDATA[
<p>Walk-in-interview for the following temporary positions will be conducted on 20th December 2014 (between 10:00 AM to 01:00 PM) at Agricultural Knowledge Management Unit, A0 block (Ground Floor), LBS Building, Indian Agricultural Research Institute, New Delhi-110012:</p>

<p>1 Dr. A.K.Mishra Coordinator &amp; PI (BTISnet)</p>

<p>Traineeship (two) for one year</p>

<p>Rs. 5000/- (consolidated)</p>

<p>M.Sc. (Bioinformatics) with 60 % marks from a recognized University</p>

<p>20-12-2014 (10:00 AM -11:00 AM)</p>

<p>Studentship (four) for one year</p>

<p>Rs. 2500/- (consolidated)</p>

<p>Final year M.Sc./ M.Tech (Bioinformatics) Students from a recognized University</p>

<p>20-12-2014 (11:00 AM- 1:00 PM)</p>

<p>The positions are purely temporary and co-terminus with the DBT Programme. Eligible candidates are requested to submit the application form in the prescribed format along with original certificates/ documents (Degree, Marks sheets, Work experience, if any) at the time of interview. No TA/DA will be paid. Maximum age limit is 28 years for all positions. Age relaxation of 5 yrs for SC/ST and woman candidates and 3 years for OBC candidates will be given. Canvassing in any form invites disqualification.</p>

<p>Advertisement: http://www.iari.res.in/files/BIC-08122014-20141208-172344.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44223/ale-assembly-likelihood-estimator</guid>
	<pubDate>Wed, 08 Mar 2023 01:39:33 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44223/ale-assembly-likelihood-estimator</link>
	<title><![CDATA[ALE: Assembly Likelihood Estimator]]></title>
	<description><![CDATA[<p>Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly.&nbsp; Depending on your genome size you may want to convert the .wig files to the BigWig format.</p><p>Address of the bookmark: <a href="https://github.com/sc932/ALE" rel="nofollow">https://github.com/sc932/ALE</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/44371/steps-to-find-all-the-repeats-in-the-genome</guid>
	<pubDate>Thu, 31 Aug 2023 02:43:28 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/44371/steps-to-find-all-the-repeats-in-the-genome</link>
	<title><![CDATA[Steps to find all the repeats in the genome !]]></title>
	<description><![CDATA[<div><p>To find repeats in a genome from 2 to 9 length using a Perl script, you can use the RepeatMasker tool with the "--length" option<a href="https://mobilednajournal.biomedcentral.com/articles/10.1186/1759-8753-5-13" target="_blank">[0]</a>. Here's a step-by-step guide:</p></div><div><ol>
<li>Install RepeatMasker: First, you need to install RepeatMasker on your system. You can download it from the RepeatMasker website<a href="https://mobilednajournal.biomedcentral.com/articles/10.1186/1759-8753-5-13" target="_blank">[0]</a>.</li>
</ol></div><div><ol>
<li>Prepare the genome sequence: Make sure you have the genome sequence in a FASTA file format. Let's assume the file is named "genome.fasta".</li>
</ol><blockquote><p>./RepeatMasker -pa &lt;number_of_processors&gt; -nolow -norna -no_is -div &lt;divergence_value&gt; -lib RepeatMaskerLib.embl -gff -xsmall -small -poly -species &lt;species_name&gt; -dir &lt;output_directory&gt; -length &lt;min_length&gt;-&lt;max_length&gt; genome.fasta</p></blockquote><div><p>Replace the following placeholders with appropriate values:</p><ul>
<li><code>&lt;number_of_processors&gt;</code>: The number of processors/threads you want to use for parallel processing.</li>
<li><code>&lt;divergence_value&gt;</code>: The divergence value for the species you are analyzing. You can find divergence values for different species in the RepeatMasker documentation<a href="https://mobilednajournal.biomedcentral.com/articles/10.1186/1759-8753-5-13" target="_blank">[0]</a>.</li>
<li><code>&lt;species_name&gt;</code>: The name of the species you are analyzing.</li>
<li><code>&lt;output_directory&gt;</code>: The directory where you want the output files to be saved.</li>
<li><code>&lt;min_length&gt;</code>&nbsp;and&nbsp;<code>&lt;max_length&gt;</code>: The minimum and maximum lengths of the repeats you want to find (in this case, 2 and 9).</li>
</ul></div><div><ol>
<li>Analyze the output: RepeatMasker will generate several output files, including a .out file. You can parse this file to extract the information you need. There is a Perl tool called "one_code_to_find_them_all.pl" that can help you parse RepeatMasker output files<a href="https://mobilednajournal.biomedcentral.com/articles/10.1186/1759-8753-5-13" target="_blank">[0]</a>. You can download it from the source provided.</li>
</ol></div><div><ol>
<li>Use the provided Perl script: Once you have the "one_code_to_find_them_all.pl" script, you can run it to conveniently parse the RepeatMasker output files. Here's an example of how to use it:</li>
</ol><blockquote><p>perl one_code_to_find_them_all.pl --rm &lt;RepeatMasker_out_file&gt; --length &lt;length_file&gt;</p></blockquote></div><p>&nbsp;</p></div><div><div><p>Replace&nbsp;<code>&lt;RepeatMasker_out_file&gt;</code>&nbsp;with the path to your RepeatMasker .out file, and&nbsp;<code>&lt;length_file&gt;</code>&nbsp;with the path to a file containing the lengths of the reference elements.</p></div><div><p>This script will generate several output files, including .log.txt and .copynumber.csv, which contain quantitative information about the identified repeat elements.</p></div><div><p>Remember to adjust the parameters and options according to your specific needs and the characteristics of your genome.</p></div></div>]]></description>
	<dc:creator>Neel</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/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome</guid>
	<pubDate>Thu, 08 Aug 2024 23:31:18 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/44637/tools-to-access-the-quality-of-your-assembled-genome</link>
	<title><![CDATA[Tools to access the quality of your assembled genome !]]></title>
	<description><![CDATA[<ul dir="auto">
<li><a href="https://github.com/linsalrob/fasta_validator">FASTA VALIDATOR</a>&nbsp;+&nbsp;<a href="https://github.com/shenwei356/seqkit">SEQKIT RMDUP</a>: FASTA validation</li>
<li><a href="https://genometools.org/tools/gt_gff3validator.html">GENOMETOOLS GT GFF3VALIDATOR</a>: GFF3 validation</li>
<li><a href="https://github.com/PlantandFoodResearch/assemblathon2-analysis/blob/a93cba25d847434f7eadc04e63b58c567c46a56d/assemblathon_stats.pl">ASSEMBLATHON STATS</a>: Assembly statistics</li>
<li><a href="https://genometools.org/tools/gt_stat.html">GENOMETOOLS GT STAT</a>: Annotation statistics</li>
<li><a href="https://github.com/ncbi/fcs">NCBI FCS ADAPTOR</a>: Adaptor contamination pass/fail</li>
<li><a href="https://github.com/ncbi/fcs">NCBI FCS GX</a>: Foreign organism contamination pass/fail</li>
<li><a href="https://gitlab.com/ezlab/busco">BUSCO</a>: Gene-space completeness estimation</li>
<li><a href="https://github.com/tolkit/telomeric-identifier">TIDK</a>: Telomere repeat identification</li>
<li><a href="https://github.com/oushujun/LTR_retriever/blob/master/LAI">LAI</a>: Continuity of repetitive sequences</li>
<li><a href="https://github.com/DerrickWood/kraken2">KRAKEN2</a>: Taxonomy classification</li>
<li><a href="https://github.com/igvteam/juicebox.js">HIC CONTACT MAP</a>: Alignment and visualisation of HiC data</li>
<li><a href="https://github.com/mummer4/mummer">MUMMER</a>&nbsp;&rarr;&nbsp;<a href="http://circos.ca/documentation/">CIRCOS</a>&nbsp;+&nbsp;<a href="https://plotly.com/">DOTPLOT</a>&nbsp;&amp;&nbsp;<a href="https://github.com/lh3/minimap2">MINIMAP2</a>&nbsp;&rarr;&nbsp;<a href="https://github.com/schneebergerlab/plotsr">PLOTSR</a>: Synteny analysis</li>
<li><a href="https://github.com/marbl/merqury">MERQURY</a>: K-mer completeness, consensus quality and phasing assessment</li>
</ul>]]></description>
	<dc:creator>LEGE</dc:creator>
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<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>
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