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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/43799?offset=280</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/44364/genbank-release-2570-is-now-available</guid>
	<pubDate>Wed, 23 Aug 2023 00:23:23 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/44364/genbank-release-2570-is-now-available</link>
	<title><![CDATA[GenBank release 257.0 is now available!]]></title>
	<description><![CDATA[<p><span>GenBank release 257.0 is now available! This release has 25.10 trillion bases and 3.69 billion records. Learn more:&nbsp;https://ncbiinsights.ncbi.nlm.nih.gov/2023/08/21/genbank-release-257/</span><a href="https://ow.ly/zHbV50PBE5o"><br /></a></p><p><a href="https://www.ncbi.nlm.nih.gov/genbank/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=genbank-release-20230821">GenBank</a>&nbsp;release 257.0 (8/15/2023) is now available on the&nbsp;<a href="https://ftp.ncbi.nlm.nih.gov/genbank/">NCBI FTP site</a>. This release has 25.10 trillion bases and 3.69 billion records.</p><p><strong>The current release has:</strong></p><ul>
<li>246,119,175 traditional records containing 2,112,058,517,945 base pairs of sequence data</li>
<li>2,631,493,489 WGS records containing 22,294,446,104,543 base pairs of sequence data</li>
<li>686,271,945 bulk-oriented TSA records containing 646,176,166,908 base pairs of sequence data</li>
<li>124,421,006 bulk-oriented TLS records containing 48,289,699,026 base pairs of sequence data</li>
</ul>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37788/s-plot2-creates-an-interactive-two-dimensional-heatmap-of-sequences</guid>
	<pubDate>Fri, 28 Sep 2018 05:36:19 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37788/s-plot2-creates-an-interactive-two-dimensional-heatmap-of-sequences</link>
	<title><![CDATA[S-plot2: creates an interactive, two-dimensional heatmap of sequences]]></title>
	<description><![CDATA[<p><span>S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can be efficiently compared. The tool includes functionality to extract, analyze, and automate BLAST queries of regions of interest within the heatmap. This facilitates the investigation of quickly evolving coding regions, novel coding regions, and laterally transferred elements.</span></p>
<p><span>http://www.putonti-lab.com/uploads/4/5/3/0/45307835/s-plot2_tutorial.pdf</span></p>
<p><span>http://journals.sagepub.com/doi/pdf/10.1177/1176934318797354</span></p><p>Address of the bookmark: <a href="https://bitbucket.org/lkalesinskas/splot" rel="nofollow">https://bitbucket.org/lkalesinskas/splot</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38452/silix-implements-an-ultra-efficient-algorithm-for-the-clustering-of-homologous-sequences</guid>
	<pubDate>Wed, 12 Dec 2018 09:22:41 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38452/silix-implements-an-ultra-efficient-algorithm-for-the-clustering-of-homologous-sequences</link>
	<title><![CDATA[SiLiX: implements an ultra-efficient algorithm for the clustering of homologous sequences]]></title>
	<description><![CDATA[<p>The software package SiLiX implements<strong>&nbsp;an ultra-efficient algorithm for the clustering of homologous sequences</strong>, based on single transitive links (<em>single linkage</em>) with alignment coverage constraints.</p>
<p>SiLiX adopts a graph-theoretical framework to interpret similarity pairs as edges of a network. A very efficient algorithm, based on the&nbsp;<em>Disjoint Sets Data Structure</em>, allows the computation of sequence families with&nbsp;<strong>low time and space requirements</strong>.</p>
<p><strong>A parallel version</strong>&nbsp;of SiLiX, based on MPI, is also available in this package and has been proved to be scalable, so that its allows the study of&nbsp;<strong>very large datasets</strong>.</p>
<p>SiLiX is already included in the analysis pipeline for&nbsp;<a href="http://pbil.univ-lyon1.fr/databases/hogenom/acceuil.php">HOGENOM</a>.</p><p>Address of the bookmark: <a href="http://lbbe.univ-lyon1.fr/SiLiX?lang=fr" rel="nofollow">http://lbbe.univ-lyon1.fr/SiLiX?lang=fr</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39872/miropeats-discovers-regions-of-sequence-similarity-amongst-any-set-of-dna-sequences</guid>
	<pubDate>Mon, 26 Aug 2019 17:55:24 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39872/miropeats-discovers-regions-of-sequence-similarity-amongst-any-set-of-dna-sequences</link>
	<title><![CDATA[Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences]]></title>
	<description><![CDATA[<p><span>Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically. Sequence similarity searching is a very general tool that forms the basis of many different biological sequence analyses but it is limited by the verbosity of traditional alignment presentation styles. Miropeats enhances the utility of conventional DNA sequence comparisons when looking at long lengths of sequence similarity by summarizing extensive large scale sequence similarities on a single page of graphics. The latest version of Miropeats can be used as a general pairwise alignment program or in its traditional role sorting out a big mess of overlapping or similar regions.</span></p><p>Address of the bookmark: <a href="http://www.littlest.co.uk/software/bioinf/old_packages/miropeats/" rel="nofollow">http://www.littlest.co.uk/software/bioinf/old_packages/miropeats/</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>
<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/27080/mrfast-micro-read-fast-alignment-search-tool</guid>
	<pubDate>Tue, 26 Apr 2016 03:50:06 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27080/mrfast-micro-read-fast-alignment-search-tool</link>
	<title><![CDATA[mrFAST:  Micro Read Fast Alignment Search Tool]]></title>
	<description><![CDATA[<p><span>mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 4+4 bp. This manual, describes how to choose the parameters and tune mrFAST with respect to the library settings. mrFAST is designed to find&nbsp;</span><strong><span style="text-decoration: underline;">'all'</span></strong><span>&nbsp; mappings for a given set of reads, however it can return one "best" map location if the relevant parameter is invoked.</span></p>
<p><span>More at&nbsp;http://mrfast.sourceforge.net/manual.html</span></p><p>Address of the bookmark: <a href="http://mrfast.sourceforge.net/manual.html" rel="nofollow">http://mrfast.sourceforge.net/manual.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/27461/maftools</guid>
	<pubDate>Sat, 21 May 2016 22:40:21 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27461/maftools</link>
	<title><![CDATA[mafTools]]></title>
	<description><![CDATA[<p><span>Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.</span></p><p>Address of the bookmark: <a href="https://github.com/dentearl/mafTools" rel="nofollow">https://github.com/dentearl/mafTools</a></p>]]></description>
	<dc:creator>Radha Agarkar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30557/speedseq</guid>
	<pubDate>Fri, 20 Jan 2017 06:05:43 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30557/speedseq</link>
	<title><![CDATA[SpeedSeq]]></title>
	<description><![CDATA[<p>A flexible framework for rapid genome analysis and interpretation</p>
<p>C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth (2015). doi:10.1038/nmeth.3505.</p>
<p><a href="http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html">http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html</a></p><p>Address of the bookmark: <a href="https://github.com/hall-lab/speedseq" rel="nofollow">https://github.com/hall-lab/speedseq</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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