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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/26587?offset=1320</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/11609/bioinformatician%E2%80%99s-pocket-reference</guid>
	<pubDate>Sun, 08 Jun 2014 09:56:58 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/11609/bioinformatician%E2%80%99s-pocket-reference</link>
	<title><![CDATA[Bioinformatician’s Pocket Reference !!]]></title>
	<description><![CDATA[<p><span>It is amusing how brain of bioinformaticians work! Learning a new programming language for days feels so much of fun that making 5 minute discussion with neighbours (unless under special circumstances!) in our own mother-tongue. Today every bioinformatician keeps more than few languages and core IT toolkits on their plate. It has become mandatory to be able to mould different code snippets to build our own custom workflows, and thus keeping syntax at our fingertips has become essential.Although Google is best way to get syntax problem solved, it is not a bad idea to keep reference sheets is our smartphones or stick out some printed sheets on the back of your door, in the old fashion way!!</span></p><p>Address of the bookmark: <a href="http://infoplatter.wordpress.com/2014/04/06/bioinformaticians-pocket-reference/" rel="nofollow">http://infoplatter.wordpress.com/2014/04/06/bioinformaticians-pocket-reference/</a></p>]]></description>
	<dc:creator>RAJESH DETROJA</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39624/cogent-a-tool-for-reconstructing-the-coding-genome-using-high-quality-full-length-transcriptome-sequences</guid>
	<pubDate>Tue, 18 Jun 2019 05:33:04 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39624/cogent-a-tool-for-reconstructing-the-coding-genome-using-high-quality-full-length-transcriptome-sequences</link>
	<title><![CDATA[Cogent: a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences.]]></title>
	<description><![CDATA[<div id="yui_3_14_1_1_1560853173251_3865">Cogent is a tool that identifies gene&nbsp;families and reconstructs the coding genome using high-quality transcriptome data without a reference genome, and can be used to check&nbsp;assemblies&nbsp;for the presence of&nbsp;these known coding sequences.</div>
<div>&nbsp;</div>
<div>
<p>Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. It is designed to be used on&nbsp;<a href="https://github.com/PacificBiosciences/cDNA_primer/wiki">Iso-Seq data</a>&nbsp;and in cases where there is no reference genome or the ref genome is highly incomplete.</p>
<p>See a&nbsp;<a href="https://www.dropbox.com/s/mn6hwhguh0pqceu/20160106_Cogent_developers_conference_slides_Cuttlefish.pdf?dl=0">recent presentation</a>&nbsp;on Cogent being applied to the Cuttlefish Iso-Seq data.</p>
<p><a href="https://www.dropbox.com/s/kz0gi7qg0w82k9a/20161026_Cogent_manuscript_forGitHub.pdf?dl=0">Cogent preliminary draft paper (updated 2016Dec version)</a>,&nbsp;<a href="https://www.dropbox.com/s/37412o8glvnfhf9/20161026_Cogent_ManuscriptPlusSupplement_forGitHub.pdf?dl=0">Supplementary</a></p>
<p>Please see&nbsp;<a href="https://github.com/Magdoll/Cogent/wiki">wiki</a>&nbsp;for details on usage.</p>
</div><p>Address of the bookmark: <a href="https://github.com/Magdoll/Cogent" rel="nofollow">https://github.com/Magdoll/Cogent</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/12218/assistant-professor-in-medical-bioinformatics</guid>
  <pubDate>Tue, 24 Jun 2014 01:46:36 -0500</pubDate>
  <link></link>
  <title><![CDATA[Assistant Professor in Medical Bioinformatics]]></title>
  <description><![CDATA[
<p>Advt. No : ME-I/A-IV/03/14<br />No.of Posts:01 (SC)<br />Pay Scale:<br />Pay Band of Rs.15600-39100 + Rs.6000/- GP +NPA @ 25% of Basic Pay +Learning Resource Allowance @ Rs.20,000/-P.A.+ Conveyance Allowance @ Rs. 1650/-P.M.+ Academic Allowance @ Rs.2500/- P.M. and other admissible allowances.<br />Qualifications:<br />Area of Specialization:-<br />Bioinformatics/Computational/Biology/Genomics/ Proteomics/ Structural Biology<br />1. Postgraduate qualification, e.g. Master’s Degree in Biotechnology/Bioinformatics/ Biophysics.<br />2. A Doctorate Degree of recognized University/Institute in a basic or allied Medical Science subject e.g. Medical Biotechnology/Biophysics. Bioinformatics/X-ray Crystallography/<br />Immunology/Structural Biology etc<br />Experience:<br />1.Minimum three years teaching and/or research experience in a recognized medical/research Institution in an allied medical subject after obtaining doctorate degree and preferably in Medical<br />Molecular Biology/ Biophysics/Structural Biology/Genomics and Clinical Proteomics/Computational Biology.<br />2. Minimum two publication with atleast one in international journal and atleast one as first author<br />Desirable:-<br />Consistently excellent scholastic/academic record, demonstrated ability to write grant proposal/(s) successfully, Post Doctoral training in a frontier area of medical Bioinformatics Research and of direct relevance to clinical diagnosis or patient care (preferably from a recognized top-ranking medical institution abroad)<br />Send your applications to O/O, Deputy Registrar, Recruitment &amp; Establishment Cell, University of Health Sciences, Rohtak by 08.7.2014<br />For more details,please visit website: http://pgimsrohtak.nic.in/2014%20AP%20Advt.pdf<br />Last Apply Date: 08 Jul 2014</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/41230/curated-set-of-ribosomal-rna-rrna-reference-sequences-targeted-loci-with-verifiable-organism</guid>
	<pubDate>Sun, 23 Feb 2020 02:17:30 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/41230/curated-set-of-ribosomal-rna-rrna-reference-sequences-targeted-loci-with-verifiable-organism</link>
	<title><![CDATA[Curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism]]></title>
	<description><![CDATA[<p>MCBI have a curated set of ribosomal RNA (rRNA) reference sequences (targeted loci) with verifiable organism sources and current names. This set is critical for correctly identifying and classifying prokaryotic (bacteria and archaea) and fungal samples. To provide easy access to these sequences, we recently added a separate rRNA/ITS databases section on the nucleotide BLAST page for these targeted sequences that makes it convenient to quickly identify source organisms. The new databases are: </p><p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *16S ribosomal RNA (Bacteria and Archaea)</p><p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *18S ribosomal RNA sequences (SSU) from Fungi type and reference material&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</p><p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *28S ribosomal RNA sequences (LSU) from Fungi type and reference material</p><p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; *Internal transcribed spacer region (ITS) from Fungi type and reference material</p><p>You can also download these from the BLAST db FTP area.&nbsp; See the <a href="https://go.usa.gov/xdEBX" target="_blank">NCBI Insights post</a> for more detail. </p><p>Useful links</p><p>-----------------</p><p><a href="https://go.usa.gov/xdEj5" target="_blank">BLAST form with rRNA/ITS databases</a></p><p><a href="https://ftp.ncbi.nlm.nih.gov/blast/db/" target="_blank">BLAST db download</a></p><p><a href="https://www.ncbi.nlm.nih.gov/refseq/targetedloci/" target="_blank">Targeted loci</a></p><p><span style="color: black;">If you have any questions or concerns, please contact <a href="mailto:blast-help@ncbi.nlm.nih.gov" target="_blank" title="Follow link">blast-help@ncbi.nlm.nih.gov<sup><span style="color: black; text-decoration: none;"><img src="https://mail.google.com/mail/u/0?ui=2&amp;ik=024a8aa0b9&amp;attid=0.1&amp;permmsgid=msg-f:1659255165855446848&amp;th=1706dbc8408bb740&amp;view=fimg&amp;sz=s0-l75-ft&amp;attbid=ANGjdJ_drW2ArYDNLoHrQh36gm6rp2Std8ZUSplCzP6bYQSQYBsQfZ_85vOujXOdTRdaLxrR7QeEBVUbyACPBJHhFUeIglX8G7Ew7TcclzhvO7fJhiz7sIdkkDgZ7QA&amp;disp=emb" alt="https://jira.ncbi.nlm.nih.gov/images/icons/mail_small.gif" width="13" height="12" style="border: 0px;"></span></sup></a></span></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/12582/postdoc-position-at-centre-mediterraneen-de-medecine-moleculaire</guid>
  <pubDate>Sun, 06 Jul 2014 11:23:06 -0500</pubDate>
  <link></link>
  <title><![CDATA[Postdoc position at Centre Méditerranéen de Médecine Moléculaire]]></title>
  <description><![CDATA[
<p>The research group of Dr. Michele Trabucchi at the Centre Méditerranéen de Médecine Moléculaire (C3M) at INSERM U1065 (University of Nice Sophia-Antipolis, France) is seeking candidates for a Postdoctoral fellow position to start on October 2014 for 3 years funded by FRM (Fondation pour la Recherche Médicale).<br />The broad interest of the lab is in understanding the expression control and function of small RNAs in activated myeloid cells (visit our webpage to check research interests and publications of the group : http://www.unice.fr/c3m/EN/Equipe10.html ). </p>

<p>The work will focus on the functional studies of small RNAs by using next-generation sequencing approaches.<br /> <br />Candidates should hold a Ph.D. degree and have strong background in bioinformatics.<br />The University of Nice Sophia-Antipolis provides a wide range of facilities and training essential for biomedical research.<br />Interested applicants should send a PDF with a cover letter stating research interests and qualifications, an updated CV, a summary of previous research experience and contact information for two references to Michele Trabucchi ( mtrabucchi@unice.fr )</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/42296/igblast-117-is-now-available-with-improved-identification-of-productive-v-gene-sequences</guid>
	<pubDate>Sun, 01 Nov 2020 16:52:58 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/42296/igblast-117-is-now-available-with-improved-identification-of-productive-v-gene-sequences</link>
	<title><![CDATA[IgBLAST 1.17 is now available with improved identification of productive V gene sequences]]></title>
	<description><![CDATA[<p>A new release of&nbsp;<a href="https://go.usa.gov/x7WMc" target="_blank">IgBLAST</a>&nbsp;(1.17), the popular package for classifying and analyzing immunoglobulin and T cell receptor sequences, is now available on the&nbsp;<a href="https://go.usa.gov/x7WMc" target="_blank">web</a>&nbsp;and from the&nbsp;<a href="https://ftp.ncbi.nih.gov/blast/executables/igblast/release/LATEST" target="_blank">FTP site</a>. The updated package is better at identifying productive V gene sequences. We added a new field , &ldquo;V frame shift&rdquo;, to the IgBLAST output to indicate whether the V gene translation frame contains a frame-shift. We have also updated the definition of a productive V(D)J sequence to now exclude those with internal frame shifts.</p><p>See the&nbsp;<a href="https://ncbi.github.io/igblast/" target="_blank">new IgBLAST manual</a>&nbsp;on the NCBI GitHub site for more information on setting up and running IgBLAST.</p><p>If you have any questions or concerns, please email us at&nbsp;<a href="mailto:blast-help@ncbi.nlm.nih.gov" target="_blank">blast-help@ncbi.nlm.nih.gov</a></p><p>&nbsp;</p>]]></description>
	<dc:creator>Jit</dc:creator>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/12870/nuclear-dynamics-lab</guid>
  <pubDate>Thu, 17 Jul 2014 15:03:27 -0500</pubDate>
  <link></link>
  <title><![CDATA[Nuclear Dynamics Lab]]></title>
  <description><![CDATA[
<p>Lab focus is to elucidate fundamental principles, new mechanisms, machineries and emergent properties that are involved in maintaining the genome and gene expression programmes for improvements in lifelong health and well-being for all.</p>

<p>More at http://www.babraham.ac.uk/our-research/nuclear-dynamics/</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44234/steps-to-find-palindrome-in-genomes</guid>
	<pubDate>Thu, 09 Mar 2023 02:56:54 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44234/steps-to-find-palindrome-in-genomes</link>
	<title><![CDATA[Steps to find palindrome in genomes !]]></title>
	<description><![CDATA[<div><div><div><div><div><div><div><div><div><div><p>Palindromes are sequences of nucleotides that read the same backward as forward. They can be present in genomes and have various biological functions. Here are some methods for discovering palindromes in genomes:</p><ol>
<li>
<p>Direct sequence search: One of the simplest ways to discover palindromes is to search the genome sequence directly for palindromic sequences using pattern matching tools, such as regular expressions or string algorithms. This approach can be useful for discovering simple palindromes, but may miss more complex palindromic structures.</p>
</li>
<li>
<p>Dot plot analysis: Dot plot analysis is a graphical method that can be used to identify palindromic regions in a genome. It involves plotting the genome sequence against itself and examining the diagonal patterns that emerge. Palindromic regions will appear as symmetrical patterns along the diagonal.</p>
</li>
<li>
<p>Restriction enzyme analysis: Some restriction enzymes, such as EcoRI and HindIII, recognize palindromic sequences and cleave DNA at these sites. By digesting the genome with these enzymes and examining the resulting fragments, palindromic regions can be identified.</p>
</li>
<li>
<p>Next-generation sequencing: High-throughput sequencing technologies, such as PacBio and Oxford Nanopore, can generate long reads that can span entire palindromic regions. By mapping these reads to the genome, palindromic regions can be identified and characterized.</p>
</li>
<li>
<p>Comparative genomics: Comparing the genomes of related species can also reveal palindromic regions that are conserved across evolutionarily divergent lineages. This approach can help identify functional palindromes that are under selective pressure.</p>
</li>
</ol><p>Overall, the discovery of palindromic sequences in genomes can be accomplished using a variety of methods, each with their own advantages and limitations. A combination of these methods can provide a comprehensive understanding of the palindromic landscape of a genome.</p></div></div></div></div></div></div></div></div></div></div>]]></description>
	<dc:creator>BioStar</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/14218/pimp-your-brain-bioinformatics</guid>
	<pubDate>Wed, 20 Aug 2014 22:09:21 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/14218/pimp-your-brain-bioinformatics</link>
	<title><![CDATA[Pimp your brain: Bioinformatics]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/KqelGy6Q8nE" frameborder="0" allowfullscreen></iframe>Jan Lisec from the Max Planck Institute of Molecular Plant Physiology explains, in this "pimp your brain" episode, what bioinformatics is and why bioinformatics is so important and indispensable for biological research.

In the video serial "Pimp your brain" scientists from the Max Planck Institute of Molecular Plant Physiology describe their research. More videos from the 'Pimp your brain' serial are available on www.youtube.com/playlist?list=PL-l9VItC9Gn2Ur2Xj6PTOAkjLUlVPbIOO

More videos are available on www.mpimp-golm.mpg.de]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44878/jaeger-an-accurate-and-fast-deep-learning-tool-to-detect-bacteriophage-sequences</guid>
	<pubDate>Thu, 14 Aug 2025 04:02:05 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44878/jaeger-an-accurate-and-fast-deep-learning-tool-to-detect-bacteriophage-sequences</link>
	<title><![CDATA[Jaeger : an accurate and fast deep-learning tool to detect bacteriophage sequences]]></title>
	<description><![CDATA[<p dir="auto">Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies.</p>
<p dir="auto">The performance of the Jaeger workflow can be significantly increased by utilizing GPUs. To enable GPU support, the CUDA Toolkit and cuDNN library must be accessible to conda.</p>
<div>
<pre><code># setup bioconda
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

# create conda environment and install jaeger
mamba create -n jaeger -c nvidia -c conda-forge cuda-nvcc "python&gt;=3.9,&lt;3.12" pip jaeger-bio


# activate environment
conda activate jaeger</code></pre>
</div><p>Address of the bookmark: <a href="https://github.com/MGXlab/Jaeger" rel="nofollow">https://github.com/MGXlab/Jaeger</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
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