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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/41405?offset=160</link>
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	<item>
	<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>
</item>
<item>
	<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>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44896/jaeger-an-accurate-and-fast-deep-learning-tool-to-detect-bacteriophage-sequences</guid>
	<pubDate>Sun, 31 Aug 2025 06:30:16 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44896/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><span>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.</span></p><p>Address of the bookmark: <a href="https://github.com/MGXlab/Jaeger" rel="nofollow">https://github.com/MGXlab/Jaeger</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/33983/web-apollo-a-web-based-genomic-annotation-editing-platform</guid>
	<pubDate>Fri, 28 Jul 2017 04:48:17 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/33983/web-apollo-a-web-based-genomic-annotation-editing-platform</link>
	<title><![CDATA[Web Apollo: a web-based genomic annotation editing platform]]></title>
	<description><![CDATA[<p><span>Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new genomes. These researchers require tools to describe the functional features of their newly sequenced genomes. With Web Apollo researchers can use any of the common browsers (for example, Chrome or Firefox) to jointly analyze and precisely describe the features of a genome in real time, whether they are in the same room or working from opposite sides of the world.</span></p><p>Address of the bookmark: <a href="http://genomearchitect.github.io/" rel="nofollow">http://genomearchitect.github.io/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35384/mgcv-the-microbial-genomic-context-viewer-for-comparative-genome-analysis</guid>
	<pubDate>Mon, 29 Jan 2018 04:55:46 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35384/mgcv-the-microbial-genomic-context-viewer-for-comparative-genome-analysis</link>
	<title><![CDATA[MGcV: the microbial genomic context viewer for comparative genome analysis]]></title>
	<description><![CDATA[<p><span>MGcV is an interactive web-based visalization tool tailored to facilitate small scale genome analysis. To start using MGcV:</span></p>
<ol>
<li>Supply your genes/genomic segments/phylogenetic tree of interest in the input-box by
<ul>
<li>selecting the type of identifier and pasting identifiers (one per line)</li>
<li><em><strong>or</strong></em>&nbsp;by using the&nbsp;<a>gene ID search tool</a></li>
<li><em><strong>or</strong></em>&nbsp;with the&nbsp;<a>BLAST search tool</a></li>
</ul>
</li>
<li>Click "Visualize context".</li>
</ol>
<p><span>Consult the&nbsp;</span><a href="http://mgcv.cmbi.ru.nl/help.html" target="_blank">documentation</a><span>&nbsp;to learn more about MGcV.</span></p><p>Address of the bookmark: <a href="http://mgcv.cmbi.ru.nl/" rel="nofollow">http://mgcv.cmbi.ru.nl/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36907/higlass-a-tool-for-exploring-genomic-contact-matrices-and-tracks</guid>
	<pubDate>Mon, 11 Jun 2018 09:44:49 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36907/higlass-a-tool-for-exploring-genomic-contact-matrices-and-tracks</link>
	<title><![CDATA[HiGlass: a tool for exploring genomic contact matrices and tracks.]]></title>
	<description><![CDATA[HiGlass is a tool for exploring genomic contact matrices and tracks. Please take a look at the examples and documentation for a description of the ways that it can be configured to explore and compare contact matrices. To load private data, HiGlass can be run locally within a Docker container. The HiC data in the examples below is from Rao et al. (2014)

http://higlass.io/<p>Address of the bookmark: <a href="http://higlass.io/" rel="nofollow">http://higlass.io/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38053/swgis-v20-a-seqword-genomic-island-sniffer</guid>
	<pubDate>Thu, 01 Nov 2018 12:35:52 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38053/swgis-v20-a-seqword-genomic-island-sniffer</link>
	<title><![CDATA[swgis v2.0 : a seqword genomic island sniffer]]></title>
	<description><![CDATA[<p><strong>swgis v2.0</strong>&nbsp;is the modified version of the seqword genomic island sniffer. this version is specifically optimized for predicting genomic islands in eukaryotic genomes. swgis v2.0 was tested on several eukaryotic species of different lineages. all identified genomic islands were deposited in the&nbsp;<a href="http://eugi.bi.up.ac.za/" title="Go to EuGI database">eugi database</a>.</p>
<p><a href="http://eugi.bi.up.ac.za/download_swgis/swgisv2.0.zip" title="Download SWGIS v2.0">download swgis v2.0</a></p><p>Address of the bookmark: <a href="http://eugi.bi.up.ac.za/eugi_download_swgis.php" rel="nofollow">http://eugi.bi.up.ac.za/eugi_download_swgis.php</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/38682/bourque-lab</guid>
  <pubDate>Mon, 14 Jan 2019 15:39:25 -0600</pubDate>
  <link></link>
  <title><![CDATA[Bourque Lab]]></title>
  <description><![CDATA[
<p>The goal of the lab is to understand mammalian genomes using comparative genomic and epigenomic analyses. Areas of interest include: the evolution of regulatory sequences, the role of transposable elements in gene regulation and the impact of genome rearrangements in evolution and cancer.</p>

<p>As a computational genomicists our work involves examining billions of DNA base pairs and interpreting how variation impacts basic biology and disease. We develop computational methods and resources for the functional annotation of genomes with a special emphasis on sequencing-based assays (e.g. ChIP-seq, RNA-Seq, exome- and whole-genome sequencing, single-cell analysis).</p>

<p>http://www.computationalgenomics.ca</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41464/phytozome-v121-plant-science-community-hub-for-accessing-palnts-genomic-data</guid>
	<pubDate>Tue, 17 Mar 2020 07:30:17 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41464/phytozome-v121-plant-science-community-hub-for-accessing-palnts-genomic-data</link>
	<title><![CDATA[Phytozome  v12.1: plant science community hub for accessing palnts genomic data]]></title>
	<description><![CDATA[<p>Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets that have been sequenced elsewhere. As of release v12.1.6, Phytozome hosts 93 assembled and annotated genomes, from 82 Viridiplantae species. More than half of these genomes have been sequenced, assembled and/or annotated with JGI Plant Science program resources. By integrating this large collection of plant genomes into a single resource and performing comprehensive and uniform annotation and analyses, Phytozome facilitates accurate and insightful comparative genomics studies.</p><p>Address of the bookmark: <a href="https://phytozome.jgi.doe.gov/pz/portal.html" rel="nofollow">https://phytozome.jgi.doe.gov/pz/portal.html</a></p>]]></description>
	<dc:creator>Surabhi Chaudhary</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44630/genofig-a-user-friendly-application-for-the-visualization-and-comparison-of-genomic-regions</guid>
	<pubDate>Mon, 05 Aug 2024 23:06:58 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44630/genofig-a-user-friendly-application-for-the-visualization-and-comparison-of-genomic-regions</link>
	<title><![CDATA[GenoFig: a user-friendly application for the visualization and comparison of genomic regions]]></title>
	<description><![CDATA[<p>Tool for graphical vizualisation of annotated genetic regions, and homologous regions comparison. It is an independent recoding of Easyfig 2 initially developped by at the S. Beatson Lab [<a href="https://mjsull.github.io/Easyfig/" target="_blank">https://mjsull.github.io/Easyfig/</a>]</p>
<p dir="auto">Download the GenoFig source code using the 'Download' button on top of this page. Cloning is currently not available for people not member of the INRAE French Institution. After decompression, open a terminal in the folder containing the decompressed files and run:</p>
<div>
<pre id="code-47"><code><span>conda env create -f extras/requirements.yml</span>
<span>extras/SETUP.sh</span></code></pre>
</div><p>Address of the bookmark: <a href="https://forgemia.inra.fr/public-pgba/genofig" rel="nofollow">https://forgemia.inra.fr/public-pgba/genofig</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

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