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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/36994?offset=50</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40212/kalign-fast-multiple-sequence-alignment-program-for-biological-sequences</guid>
	<pubDate>Fri, 01 Nov 2019 00:20:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40212/kalign-fast-multiple-sequence-alignment-program-for-biological-sequences</link>
	<title><![CDATA[Kalign: fast multiple sequence alignment program for biological sequences.]]></title>
	<description><![CDATA[<p><span>Kalign is a fast multiple sequence alignment program for biological sequences.</span></p>
<p>Align sequences and output the alignment in MSF format:</p>
<pre><code>kalign -i BB11001.tfa -f msf  -o out.msf
</code></pre>
<p>Align sequences and output the alignment in clustal format:</p>
<pre><code>kalign -i BB11001.tfa -f clu -o out.clu
</code></pre>
<p>Re-align sequences in an existing alignment:</p>
<pre><code>kalign -i BB11001.msf  -o out.afa
</code></pre>
<p>Reformat existing alignment:</p>
<pre><code>kalign -i BB11001.msf -r afa -o out.afa</code></pre><p>Address of the bookmark: <a href="https://github.com/TimoLassmann/kalign" rel="nofollow">https://github.com/TimoLassmann/kalign</a></p>]]></description>
	<dc:creator>BioStar</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/38526/versatile-genome-assembly-evaluation-with-quast-lg</guid>
	<pubDate>Fri, 21 Dec 2018 22:06:31 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38526/versatile-genome-assembly-evaluation-with-quast-lg</link>
	<title><![CDATA[Versatile genome assembly evaluation with QUAST-LG]]></title>
	<description><![CDATA[<p>QUAST-LG is an extension of&nbsp;<a href="http://cab.spbu.ru/software/quast/">QUAST</a>&nbsp;intended for evaluating large-scale genome assemblies (up to mammalian-size).</p>
<p>QUAST-LG&nbsp;is included in the QUAST&nbsp; package starting from version 5.0.0 (<a href="https://sourceforge.net/projects/quast/files/latest/download?source=files">download the latest release</a>). Run QUAST as usual and do not forget to add&nbsp;<span>‐‐large</span>&nbsp;option to your command!</p>
<p>A short list of the new features (see&nbsp;<a href="http://cab.spbu.ru/files/quast/latest-docs/CHANGES.txt">CHANGES</a>&nbsp;for all):</p>
<ul>
<li>Significant speedup achieved by both&nbsp;use of new fast aligner (<a href="https://github.com/lh3/minimap2">minimap2</a>) and the refactoring of alignment analyzing&nbsp;modules</li>
<li>New k-mer-based completeness and correctness metrics</li>
<li>BUSCO added for enhanced reference-free analysis</li>
<li>The concept of upper bound&nbsp;assembly (theoretical limits on the assembly&nbsp;completeness and&nbsp;contiguity for a given genome and set of reads)</li>
</ul><p>Address of the bookmark: <a href="http://cab.spbu.ru/software/quast-lg/" rel="nofollow">http://cab.spbu.ru/software/quast-lg/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41033/clark-fast-accurate-and-versatile-sequence-classification-system</guid>
	<pubDate>Sat, 15 Feb 2020 01:49:01 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41033/clark-fast-accurate-and-versatile-sequence-classification-system</link>
	<title><![CDATA[CLARK: Fast, accurate and versatile sequence classification system]]></title>
	<description><![CDATA[<p><span></span><a href="http://dx.doi.org/10.1186/s12864-015-1419-2"><strong>CLARK</strong></a><span>, a method based on a supervised sequence classification using discriminative&nbsp;</span><em>k</em><span>-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to known bacterial genomes, and (2) the assignment of BAC clones and transcript to chromosome arms/centromeres (in the absence of a finished assembly for the reference genome), CLARK outperforms in classification speed and precision the best state-of-the-art methods.</span></p>
<p><span><a href="http://clark.cs.ucr.edu/Spaced/">http://clark.cs.ucr.edu/Spaced/</a></span></p><p>Address of the bookmark: <a href="http://clark.cs.ucr.edu/Spaced/" rel="nofollow">http://clark.cs.ucr.edu/Spaced/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43856/puffaligner-a-fast-efficient-and-accurate-aligner-based-on-the-pufferfish-index</guid>
	<pubDate>Thu, 21 Apr 2022 05:41:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43856/puffaligner-a-fast-efficient-and-accurate-aligner-based-on-the-pufferfish-index</link>
	<title><![CDATA[PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index]]></title>
	<description><![CDATA[<p><span>PuffAligner, a fast, accurate and versatile aligner built on top of the Pufferfish index. PuffAligner is able to produce highly sensitive alignments, similar to those of Bowtie2, but much more quickly. While exhibiting similar speed to the ultrafast STAR aligner, PuffAligner requires considerably less memory to construct its index and align reads. PuffAligner strikes a desirable balance with respect to the time, space and accuracy tradeoffs made by different alignment tools and provides a promising foundation on which to test new alignment ideas over large collections of sequences.</span></p><p>Address of the bookmark: <a href="https://github.com/COMBINE-lab/pufferfish/tree/cigar-strings" rel="nofollow">https://github.com/COMBINE-lab/pufferfish/tree/cigar-strings</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44555/ultra-ultra-locates-tandemly-repetitive-areas-effective-labeling-of-repetitive-genomic-sequence</guid>
	<pubDate>Sat, 08 Jun 2024 16:03:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44555/ultra-ultra-locates-tandemly-repetitive-areas-effective-labeling-of-repetitive-genomic-sequence</link>
	<title><![CDATA[ULTRA (ULTRA Locates Tandemly Repetitive Areas) : Effective Labeling of Repetitive Genomic Sequence]]></title>
	<description><![CDATA[<p dir="auto">ULTRA is a tool to find and annotate tandem repeats inside genomic sequence. It is able to find repeats of any length and of any period (up to a maximum period of 4000). It can find highly decayed repeats missed by other software, and it will also be able to find very large repeats in highly repetitive sequence, regardless of the size of sequence or length of repeats. ULTRA offers meaningful annotation scores and can produce annotation P-values at user request.</p>
<p dir="auto">More at&nbsp;https://www.biorxiv.org/content/10.1101/2024.06.03.597269v1</p><p>Address of the bookmark: <a href="https://github.com/TravisWheelerLab/ULTRA" rel="nofollow">https://github.com/TravisWheelerLab/ULTRA</a></p>]]></description>
	<dc:creator>Abhi</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>

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