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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/31568?offset=1560</link>
	<atom:link href="https://bioinformaticsonline.com/related/31568?offset=1560" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/21934/ra-bioinformatics-at-bose-institute</guid>
  <pubDate>Tue, 07 Apr 2015 03:30:25 -0500</pubDate>
  <link></link>
  <title><![CDATA[RA Bioinformatics at Bose Institute]]></title>
  <description><![CDATA[
<p>Bose Institute, Kolkata, invites online applications from Indian Citizens for recruitment of Research Associate (05 posts) under Institute Plan Programmes : Improvement of Plants : Biotechnological, Genomic and Proteomic Approaches (programme No. – I), Bioinformatics and Computational Biology (programme No. – III), Microbial Genomics and Infection Biology (programme No. – V) and Basic &amp; Applied Problems in Physical and Environmental Sciences (programme No. – VII). All the posts are tenable for one (01) year.</p>

<p>ESSENTIAL QUALIFICATION: PH.D. DEGREE IN LIFE SCIENCES / PHYSICAL SCIENCE.</p>

<p>Research Associate for Programme No. –I Specialization in the area of plant molecular biology or plant proteomic study or plant pathogen interaction.<br />Research Associate for Programme No. –I Specialization in the area of plant / fungal Biotechnology, tissue culture and molecular biology<br />Research Associate for Programme No. –III Specialization in the area of structural biology and protein crystallography.<br />Research Associate for Programme No. – V Specialization in the area of microbial physiology (metabolism) or environmental microbiology, with experience in microbial genomics and proteomics.<br />Research Associate for Programme No. – VII Specialization in the area of Theoretical High Energy Astrophysics or Astroparticle Physics. Proven record of independent research experience in Astrophysical<br />Radiation Magnetohydrodynamics or Cosmic Ray Astrophysics. Experience in numerical techniques and /or date analysis would be additional advantage.<br />Associateship : 22,000/- p.m., plus admissible H.R.A. and Medical benefit.<br />Age: Below 3 Age : Below 35 years (Relaxable in case of SC/ST/OBC/Women candidates only as per rule).<br />SELECTION PROCEDURE FOR BOSE INSTITUTE- RESEARCH ASSOCIATE POST:</p>

<p>Candidates can apply on or before 13/4/2015.<br />No detailed information about the selection procedure is mentioned in the recruitment notification.<br />HOW TO APPLY FOR RESEARCH ASSOCIATE VACANCY IN BOSE INSTITUTE:</p>

<p>Interested and eligible candidates may read the application procedures and instructions carefully before applying through online as well as submitting the hard copy of the same. Candidates those who has submitted their Ph.D. Thesis and can produce Provisional Ph.D. Certificate at the time of Interview may also apply </p>

<p>Ref<br />Bose Institute Recruitment 2015 –  ADVT. NO. : BI/IF/35/2014-15.</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/poll/view/21982/which-bioinformatics-journals-do-you-follow</guid>
	<pubDate>Fri, 10 Apr 2015 12:10:21 -0500</pubDate>
	<link>https://bioinformaticsonline.com/poll/view/21982/which-bioinformatics-journals-do-you-follow</link>
	<title><![CDATA[Which Bioinformatics Journals Do You Follow?]]></title>
	<description><![CDATA[<p><span><span>Which are your favorite bioinformatics journals? The ones that you check every month or so, or that you are subscribed to?</span></span></p>]]></description>
	<dc:creator>Tenzin Paul</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/22028/walk-in-for-research-asst-programmer-enterovirus-research-centre-mumbai-india</guid>
  <pubDate>Tue, 14 Apr 2015 12:36:51 -0500</pubDate>
  <link></link>
  <title><![CDATA[Walk in for Research Asst &amp; Programmer Enterovirus Research Centre Mumbai - India]]></title>
  <description><![CDATA[
<p>Enterovirus Research Centre Mumbai Jobs 2015 –</p>

<p>Walk in for Research Asst &amp; Programmer Posts: Enterovirus Research Centre, Mumbai, Indian Council of Medical Research has issued notification for the recruitment of Research Asst &amp; Programmer vacancies on temporary basis for the project entitled “An Atlas of Non-Polio Enterovirus Types Isolated from Cases of Acute Flaccid Paralysis in India”. Eligible candidates may walk in on 20-04-2015 from 10:00 AM to 12:00 Noon. Other details like age limit, educational qualification, how to apply are given below…</p>

<p>Enterovirus Research Centre Mumbai Vacancy Details:<br />Total No. of Posts: 04<br />Name of the Posts:<br />1. Research Assistant: 03 Posts<br />2. Programmer: 01 Post</p>

<p>Age Limit: Candidates age should below 28 years. Age relaxations are applicable as per rules.</p>

<p>Educational Qualification: Candidates should have M.Sc (1st Class) in Microbiology/ Bioinformatics/ Biotechnology/ Life Science for post 1, BE/ B.Tech/ MCA for post 2.</p>

<p>Selection Process: Candidates are selected based on their performance in interview.</p>

<p>How to Apply: Eligible candidates may attend for interview along with original certificates, CV, attested copies of relevant certificates, one recent passport size photograph duly affixed on right side of application at Enterovirus Research Centre, Mumbai, Indian Council of Medical Research, Haffkine Institute Cmpound, Acharya Donde Marg, Parel, Mumbai-400012 on 20-04-2015 from 10:00 AM to 12:00 Noon.</p>

<p>Important Dates:<br />Date &amp; Time of Interview: 20-04-2015 from 10:00 AM to 12:00 Noon.<br />Registration Time: 12:00 Noon.</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/file/view/22050/binc-sample-question-paper</guid>
	<pubDate>Thu, 16 Apr 2015 09:15:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/22050/binc-sample-question-paper</link>
	<title><![CDATA[BINC Sample Question Paper !!!]]></title>
	<description><![CDATA[<p>BINC sample question paper round THREE ...</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/22050" length="316" type="text/plain" />
</item>
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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/22130/senior-research-fellow-srf-bioinformatics-at-central-institute-for-research-on-buffaloes</guid>
  <pubDate>Sat, 18 Apr 2015 04:30:47 -0500</pubDate>
  <link></link>
  <title><![CDATA[Senior Research Fellow (SRF) Bioinformatics at Central Institute for Research on Buffaloes]]></title>
  <description><![CDATA[
<p>Senior Research Fellow (SRF) Bioinformatics at Central Institute for Research on Buffaloes<br />Address: Central Institute for Research on Buffaloes, Sirsa Road, Hisar<br />State: Haryana<br />Pay Scale: Post Graduate in subjects other than Veterinary Science Rs. 16000/- per month for 1st and 2nd year and Rs. 18000/- per month for 3rd year. Post Graduate in Veterinary Science Rs. 18000/- per month for 1st and 2nd Year and Rs. 20000/- per month for 3rd year.<br />Educational Requirements: Master’s degree in biotechnology/animal biotechnology, veterinary/animal biochemistry, veterinary microbiology or veterinary/animal physiology/Nano Technology/Bioinformatics or related area.<br />Qualifications: Ph.D in relevant field/experience of working in any research project<br />Details will be available at: http://www.cirb.res.in/attachments/195_Walk-in-Interview%20for%20Senior%20Research%20Fellow%20%28SRF%29%20%28On%20Dated%2020.4.2015%29.pdf<br />How To Apply: Interested candidates who fulfill the above conditions should report for interview with a copy of their bio-data, photocopy and original certificates and testimonials, other related material i.e. reports, documents, articles, etc., if any.<br />Date &amp; Time of Interview: 20.04.2015 at 11.00 hrs<br />Venue: CIRB, Hisar</p>
]]></description>
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<item>
	<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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