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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/39624?offset=100</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38501/fgenesh-program-for-predicting-multiple-genes-in-genomic-dna-sequences</guid>
	<pubDate>Thu, 20 Dec 2018 11:55:08 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38501/fgenesh-program-for-predicting-multiple-genes-in-genomic-dna-sequences</link>
	<title><![CDATA[FGENESH - Program for predicting multiple genes in genomic DNA sequences]]></title>
	<description><![CDATA[<p>FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu&nbsp;<em>et al</em>. (2002) Science 296:79) and was used to produce 87% of all high-evidence predicted genes (Goff&nbsp;<em>et al</em>. (2002) Science 296:79).</p><p>Address of the bookmark: <a href="http://www.softberry.com/berry.phtml?topic=fgenesh&amp;group=help&amp;subgroup=gfind" rel="nofollow">http://www.softberry.com/berry.phtml?topic=fgenesh&amp;group=help&amp;subgroup=gfind</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<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/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>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/26252/recombination-detection-tool</guid>
	<pubDate>Tue, 02 Feb 2016 10:11:14 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26252/recombination-detection-tool</link>
	<title><![CDATA[Recombination detection tool]]></title>
	<description><![CDATA[<p>A program to detect recombination hotspots using population genetic data.</p>
<p>More at https://github.com/auton1/LDhot</p><p>Address of the bookmark: <a href="https://github.com/auton1/LDhot" rel="nofollow">https://github.com/auton1/LDhot</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/27311/release-notes-for-genome-workbench-2105</guid>
	<pubDate>Thu, 12 May 2016 13:49:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/27311/release-notes-for-genome-workbench-2105</link>
	<title><![CDATA[Release Notes for Genome Workbench 2.10.5]]></title>
	<description><![CDATA[<p>New Features in latest release</p><ul>
<li>New ProSplign tool integrated with Genome Workbench (<a href="https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial13">Tutorial</a>,&nbsp;<a href="https://www.youtube.com/watch?v=V9UqKJprzAg&amp;feature=youtu.be" target="_blank">Video</a>)</li>
<li>New export function for BAM/cSRA coverage graphs (<a href="https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial14">Tutorial</a>)</li>
<li>New export function for alignments GFF3 format ((<a href="https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial15">Tutorial</a>))</li>
<li>Tree View: implemented new export mode based on selections (tutorial coming)</li>
<li>Tree View: added support for&nbsp;<a href="https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial3/#distance_based_circular_trees">distance based circular trees</a></li>
<li>Tree View: new rooting mode (Midpoint Root) results in more balanced trees (<a href="https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial3#reroot_tree">Tutorial</a>)</li>
<li>Tree View: added possibility to right-click on an edge between two nodes and "Place Root at Middle of Branch" &ndash; to re-root at mid-branch (<a href="https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial3#reroot_tree">Tutorial</a>)</li>
</ul>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/27432/gkno</guid>
	<pubDate>Fri, 20 May 2016 18:56:37 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27432/gkno</link>
	<title><![CDATA[GKNO]]></title>
	<description><![CDATA[<p><span>gkno opens the world of complex bioinformatic analysis to people of all level of computational expertise. This site contains documentation, tutorials and information on all the tools that comprise gkno.</span></p>
<p><span>http://gkno.me/how-to/install.html</span></p>
<p><span>http://gkno.me/software.html</span></p><p>Address of the bookmark: <a href="http://gkno.me/" rel="nofollow">http://gkno.me/</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/27839/lorma-a-tool-for-correcting-sequencing-errors-in-long-reads-such-those-produced-by-pacific-biosciences-sequencing-machines</guid>
	<pubDate>Wed, 15 Jun 2016 17:18:36 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27839/lorma-a-tool-for-correcting-sequencing-errors-in-long-reads-such-those-produced-by-pacific-biosciences-sequencing-machines</link>
	<title><![CDATA[LoRMA: a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines]]></title>
	<description><![CDATA[<p>LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines.</p>
<p>Publication:</p>
<ul>
<li>L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de Bruijn graphs. Accepted to RECOMB-Seq 2016.</li>
</ul>
<p>Download:</p>
<ul>
<li><a href="https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/LoRMA-0.3.tar.gz">LoRMA 0.3 source files</a></li>
<li><a href="https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/README.txt">README</a></li>
</ul><p>Address of the bookmark: <a href="https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/" rel="nofollow">https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30680/easybuild</guid>
	<pubDate>Fri, 27 Jan 2017 16:00:43 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30680/easybuild</link>
	<title><![CDATA[EasyBuild]]></title>
	<description><![CDATA[<p><a href="https://github.com/hpcugent/easybuild">EasyBuild</a><span>&nbsp;is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.</span><br><span>A full list of supported software packages is available&nbsp;</span><a href="http://easybuild.readthedocs.io/en/latest/version-specific/Supported_software.html">here</a><span>.</span></p><p>Address of the bookmark: <a href="https://hpcugent.github.io/easybuild/" rel="nofollow">https://hpcugent.github.io/easybuild/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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