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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/43799?offset=260</link>
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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/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/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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/2759/dynamic-programming-alignment</guid>
	<pubDate>Thu, 22 Aug 2013 09:38:28 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/2759/dynamic-programming-alignment</link>
	<title><![CDATA[Dynamic Programming Alignment]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/EWJnDMKBEv0" frameborder="0" allowfullscreen></iframe>lecture 9, Chem. C100, Spring 2013, UCLA]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/27333/satsuma-highly-sensitive-whole-genome-synteny-alignments</guid>
	<pubDate>Fri, 13 May 2016 05:25:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27333/satsuma-highly-sensitive-whole-genome-synteny-alignments</link>
	<title><![CDATA[SATSUMA : Highly sensitive whole-genome synteny alignments.]]></title>
	<description><![CDATA[<p>Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences. Satsuma does not require any pre-processing, such as repeat masking, since it will automatically detect ambiguous mappings.<br> <br> Satsuma has parallelization built-in and is designed to run on multi-core architectures. The run-time for aligning two bird-size genomes (~1.2 Gb) is around two days on 24 CPUs. <br> <br> You can find the manual <a href="http://satsuma.sourceforge.net/manual.html">here</a>.<br> Download the latest source code from <a href="https://sourceforge.net/projects/satsuma/">here.</a><br> Stable versions can also be downloaded from the <a href="https://www.broadinstitute.org/science/programs/genome-biology/spines">Broad Institute's</a> web site.<br> <br> An incomplete list of questions and answers (yes, these have really been asked by our users! Please feel free to add your own by e-mailing us) is <a href="http://satsuma.sourceforge.net/faq.html">here</a>.<br> <br> If you use Satsuma in your research, please cite:<br> <a href="http://bioinformatics.oxfordjournals.org/content/26/9/1145.long">Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alf&ouml;ldi, J., Di Palma, F., &amp; Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics, 26(9), 1145-51</a>.</p>
<p><strong>Tutorial at http://evomics.org/learning/genomics/satsuma/</strong></p><p>Address of the bookmark: <a href="http://satsuma.sourceforge.net/" rel="nofollow">http://satsuma.sourceforge.net/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30555/yaha</guid>
	<pubDate>Fri, 20 Jan 2017 05:38:05 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30555/yaha</link>
	<title><![CDATA[YAHA]]></title>
	<description><![CDATA[<p>YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments. Unlike other aligners that report all, or one, alignment per query, or that use simple heuristics to select alignments, YAHA uses a directed acyclic graph to find the optimal set of alignments that cover a query using a biologically relevant breakpoint penalty. YAHA can also report multiple mappings per defined segment of the query. We show that YAHA detects more breakpoints in less time than BWA-SW across all SV classes, and especially excels at complex SVs comprising multiple breakpoints.</p>
<p><strong>Availability:</strong> YAHA is currently supported on 64-bit Linux systems. Binaries and sample data are freely available for download from <a href="http://faculty.virginia.edu/irahall/YAHA" target="pmc_ext">http://faculty.virginia.edu/irahall/YAHA</a>.</p>
<p><strong>Contact:</strong></p>
<p>http://genome.wustl.edu/people/groups/detail/hall-lab/</p><p>Address of the bookmark: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463118/" rel="nofollow">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463118/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32633/a-post-assembly-genome-improvement-toolkit-pagit-to-obtain-annotated-genomes-from-contigs</guid>
	<pubDate>Fri, 12 May 2017 10:50:29 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32633/a-post-assembly-genome-improvement-toolkit-pagit-to-obtain-annotated-genomes-from-contigs</link>
	<title><![CDATA[A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs]]></title>
	<description><![CDATA[<p>PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed:</p>
<p><a href="https://sourceforge.net/projects/abacas/files/">ABACAS</a>, that is able to contiguate contigs from a de novo assembly against a closely related reference.</p>
<p><a href="https://sourceforge.net/projects/image2/files/">IMAGE</a>, an iterative approach for closing gaps in assembled genomes using mate pair information. It is able to close gaps left open by the assembler in a draft genome, even when using the same data sets as used by the original assembler.</p>
<p><a href="http://icorn.sourceforge.net/">iCORN</a>, that enables errors in the consensus sequence to be corrected by iteratively mapping reads to the current assembly. An improved version, especially correction Pacfic Bioscience assemblies (PacBio) can be found&nbsp;<a href="ftp://ftp.sanger.ac.uk/pub4/resources/software/pagit/ICORN2/icorn2.V0.95.tgz">here</a>.</p>
<p><a href="https://ratt.svn.sourceforge.net/svnroot/ratt">RATT</a>, a tool to transfer the annotation from a reference genome, or an earlier assembly, onto the latest assembly.</p>
<p>PAGIT bundles these software and makes them more accessible for users.</p><p>Address of the bookmark: <a href="http://www.sanger.ac.uk/science/tools/pagit" rel="nofollow">http://www.sanger.ac.uk/science/tools/pagit</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/33006/avid-a-global-alignment-program</guid>
	<pubDate>Wed, 24 May 2017 05:19:28 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/33006/avid-a-global-alignment-program</link>
	<title><![CDATA[AVID: A Global Alignment Program]]></title>
	<description><![CDATA[<p>A new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large syntenic genomic regions and whole genome human/mouse alignments. We have also performed a quantitative comparison of AVID with other popular alignment tools. To this end, we have established a format for the representation of alignments and methods for their comparison. These formats and methods should be useful for future studies. The tools we have developed for the alignment comparisons, as well as the AVID program, are publicly available. See Web Site References section for AVID Web address and Web addresses for other programs discussed in this paper.</p><p>Address of the bookmark: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430967/" rel="nofollow">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC430967/</a></p>]]></description>
	<dc:creator>Archana Malhotra</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36216/crusview</guid>
	<pubDate>Thu, 12 Apr 2018 09:22:03 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36216/crusview</link>
	<title><![CDATA[CrusView]]></title>
	<description><![CDATA[<p><span>CrusView&nbsp;is a java based tool for karyotype/genome visualization and comparison of crucifer&nbsp;Species. It also integrates an binary version of KGBassembler and a&nbsp;post-modification step for its assembling result.</span></p><p>Address of the bookmark: <a href="http://www.cmbb.arizona.edu/?page_id=250" rel="nofollow">http://www.cmbb.arizona.edu/?page_id=250</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44559/metagraph-ultra-scalable-framework-for-dna-search-alignment-assembly</guid>
	<pubDate>Sat, 08 Jun 2024 16:15:25 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44559/metagraph-ultra-scalable-framework-for-dna-search-alignment-assembly</link>
	<title><![CDATA[MetaGraph: Ultra Scalable Framework for DNA Search, Alignment, Assembly]]></title>
	<description><![CDATA[<p><span>The MetaGraph framework</span><span>&nbsp;is designed to work with a wide range of input data sets, indexing from a few samples up to the contents of entire archives with hundreds of thousands of records. The indexing workflow always follows the same principle, transforming single input samples into error-removed, refined sample graphs, which are then merged into a joint metagraph index. Each input sample is annotated in the joint index as a subgraph. This graph index enriched with metadata can then be used for downstream applications such as&nbsp;</span><a href="https://metagraph.ethz.ch/#query">sequence search</a><span>&nbsp;or&nbsp;</span><a href="https://metagraph.ethz.ch/#assembly">differential assembly</a><span>.</span></p>
<p><span>Searcg link&nbsp;https://metagraph.ethz.ch/search&nbsp;</span></p>
<p><span>Pre-print&nbsp;https://www.biorxiv.org/content/10.1101/2020.10.01.322164v4&nbsp;</span></p><p>Address of the bookmark: <a href="https://metagraph.ethz.ch/" rel="nofollow">https://metagraph.ethz.ch/</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
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