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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/41602?offset=20</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38385/decipher-a-software-toolset-for-deciphering-and-managing-biological-sequences-efficiently-using-the-r</guid>
	<pubDate>Sun, 09 Dec 2018 19:06:17 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38385/decipher-a-software-toolset-for-deciphering-and-managing-biological-sequences-efficiently-using-the-r</link>
	<title><![CDATA[DECIPHER; a software toolset for deciphering and managing biological sequences efficiently using the R]]></title>
	<description><![CDATA[<p><span>DECIPHER is a software toolset that can be used for deciphering and managing biological sequences efficiently using the&nbsp;</span><a href="http://www.r-project.org/">R</a><span>&nbsp;programming language. The&nbsp;</span><a href="http://www.r-project.org/">R</a><span>&nbsp;package is distributed as platform independent source code under the&nbsp;</span><a href="http://www.gnu.org/copyleft/gpl.html">GPL version 3 license</a><span>. Some functionality of the program is accessible online through web tools.</span></p>
<p><span style="font-size: medium; text-align: justify;">&nbsp;</span></p><p>Address of the bookmark: <a href="http://www2.decipher.codes/" rel="nofollow">http://www2.decipher.codes/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39624/cogent-a-tool-for-reconstructing-the-coding-genome-using-high-quality-full-length-transcriptome-sequences</guid>
	<pubDate>Tue, 18 Jun 2019 05:33:04 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39624/cogent-a-tool-for-reconstructing-the-coding-genome-using-high-quality-full-length-transcriptome-sequences</link>
	<title><![CDATA[Cogent: a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences.]]></title>
	<description><![CDATA[<div id="yui_3_14_1_1_1560853173251_3865">Cogent is a tool that identifies gene&nbsp;families and reconstructs the coding genome using high-quality transcriptome data without a reference genome, and can be used to check&nbsp;assemblies&nbsp;for the presence of&nbsp;these known coding sequences.</div>
<div>&nbsp;</div>
<div>
<p>Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences. It is designed to be used on&nbsp;<a href="https://github.com/PacificBiosciences/cDNA_primer/wiki">Iso-Seq data</a>&nbsp;and in cases where there is no reference genome or the ref genome is highly incomplete.</p>
<p>See a&nbsp;<a href="https://www.dropbox.com/s/mn6hwhguh0pqceu/20160106_Cogent_developers_conference_slides_Cuttlefish.pdf?dl=0">recent presentation</a>&nbsp;on Cogent being applied to the Cuttlefish Iso-Seq data.</p>
<p><a href="https://www.dropbox.com/s/kz0gi7qg0w82k9a/20161026_Cogent_manuscript_forGitHub.pdf?dl=0">Cogent preliminary draft paper (updated 2016Dec version)</a>,&nbsp;<a href="https://www.dropbox.com/s/37412o8glvnfhf9/20161026_Cogent_ManuscriptPlusSupplement_forGitHub.pdf?dl=0">Supplementary</a></p>
<p>Please see&nbsp;<a href="https://github.com/Magdoll/Cogent/wiki">wiki</a>&nbsp;for details on usage.</p>
</div><p>Address of the bookmark: <a href="https://github.com/Magdoll/Cogent" rel="nofollow">https://github.com/Magdoll/Cogent</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41405/sequence-tube-maps-displays-multiple-genomic-sequences-in-the-form-of-a-tube-map</guid>
	<pubDate>Wed, 11 Mar 2020 01:12:06 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41405/sequence-tube-maps-displays-multiple-genomic-sequences-in-the-form-of-a-tube-map</link>
	<title><![CDATA[Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map]]></title>
	<description><![CDATA[<p>A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with <a href="https://github.com/vgteam/vg">vg</a>. (<a href="https://github.com/vgteam/vg">https://github.com/vgteam/vg</a>)</p>
<h3>Link to working demo: <a href="https://vgteam.github.io/sequenceTubeMap/">https://vgteam.github.io/sequenceTubeMap/</a></h3>
<p><img src="https://raw.githubusercontent.com/vgteam/sequenceTubeMap/master/images/header.png" alt="image" style="border: 0px; border: 0px;"></p><p>Address of the bookmark: <a href="https://github.com/vgteam/sequenceTubeMap" rel="nofollow">https://github.com/vgteam/sequenceTubeMap</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
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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/39017/macse-multiple-alignment-of-coding-sequences-accounting-for-frameshifts-and-stop-codons</guid>
	<pubDate>Mon, 18 Feb 2019 04:21:50 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39017/macse-multiple-alignment-of-coding-sequences-accounting-for-frameshifts-and-stop-codons</link>
	<title><![CDATA[MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons]]></title>
	<description><![CDATA[<p>MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.</p>
<p>For further details about the underlying algorithm see the original publication:<br><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0022594" target="_new">MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.<br>Vincent Ranwez, S&eacute;bastien Harispe, Fr&eacute;d&eacute;ric Delsuc, Emmanuel JP Douzery<br>PLoS One 2011, 6(9): e22594</a>.</p><p>Address of the bookmark: <a href="https://bioweb.supagro.inra.fr/macse/index.php?menu=releases" rel="nofollow">https://bioweb.supagro.inra.fr/macse/index.php?menu=releases</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/26303/maker</guid>
	<pubDate>Sun, 07 Feb 2016 15:59:24 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26303/maker</link>
	<title><![CDATA[MAKER]]></title>
	<description><![CDATA[<p>MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values.</p>
<p>More at http://www.yandell-lab.org/software/maker.html</p><p>Address of the bookmark: <a href="http://www.yandell-lab.org/software/maker.html" rel="nofollow">http://www.yandell-lab.org/software/maker.html</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/26375/ncbi-remap</guid>
	<pubDate>Thu, 11 Feb 2016 11:02:26 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26375/ncbi-remap</link>
	<title><![CDATA[NCBI Remap]]></title>
	<description><![CDATA[<p><span><span><strong>NCBI Remap</strong>. This tool is conceptually similar to liftOver in that in manages conversions between a pair of genome assemblies but it uses different methods to achieve these mappings. It is also available through a simple <a href="http://www.ncbi.nlm.nih.gov/genome/tools/remap">web interface</a> or you can use the <a href="http://www.ncbi.nlm.nih.gov/genome/tools/remap/docs/api">API for NCBI Remap</a>.</span></span></p>
<p><span><span>More at http://www.ncbi.nlm.nih.gov/genome/tools/remap</span></span></p>
<p><span><span>API http://www.ncbi.nlm.nih.gov/genome/tools/remap/docs/api</span></span></p><p>Address of the bookmark: <a href="http://www.ncbi.nlm.nih.gov/genome/tools/remap" rel="nofollow">http://www.ncbi.nlm.nih.gov/genome/tools/remap</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/28870/genemania</guid>
	<pubDate>Mon, 22 Aug 2016 09:55:16 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/28870/genemania</link>
	<title><![CDATA[GeneMANIA]]></title>
	<description><![CDATA[<p>Faster, more accurate algorithms function prediction "GeneMANIA (Multiple Association Network Integration Algorithm)" have however been developed in recent years and are publicly available on the web, indicating the future direction of function prediction.</p><p>Address of the bookmark: <a href="http://genemania.org/" rel="nofollow">http://genemania.org/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/32485/bacterial-genome-assembly</guid>
	<pubDate>Fri, 05 May 2017 06:11:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32485/bacterial-genome-assembly</link>
	<title><![CDATA[Bacterial genome assembly !!]]></title>
	<description><![CDATA[<p>This tutorial will serve as an example of how to use free and open-source genome assembly and secondary scaffolding tools to generate high quality assemblies of&nbsp;bacterial sequence data. The bacterial sample used in this tutorial will be referred&nbsp;to simply&nbsp;as &ldquo;Species&rdquo; since it is&nbsp;live data. This data is paired-end data, meaning that there are forward and reverse reads, which we will designate as Sample_R1.fastq and Sample_R2.fastq, respectively.</p>
<p>https://github.com/jennomics/WorkflowPaper/blob/master/Genome%20Assembly%20and%20Annotation.md</p><p>Address of the bookmark: <a href="http://bioinformatics.uconn.edu/bacterial-genome-assembly-tutorial/" rel="nofollow">http://bioinformatics.uconn.edu/bacterial-genome-assembly-tutorial/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/33691/annotationsketch</guid>
	<pubDate>Sun, 25 Jun 2017 17:54:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/33691/annotationsketch</link>
	<title><![CDATA[AnnotationSketch]]></title>
	<description><![CDATA[<p><span>The&nbsp;</span><em>AnnotationSketch</em><span>&nbsp;module is a versatile and efficient C-based drawing library for GFF3-compatible genomic annotations. It is included in the&nbsp;</span><em>GenomeTools</em><span>&nbsp;</span><a href="http://genometools.org/pub">distribution</a><span>. Additionally, bindings to the&nbsp;</span><a href="http://www.lua.org/">Lua</a><span>,&nbsp;</span><a href="http://www.python.org/">Python</a><span>&nbsp;and&nbsp;</span><a href="http://www.ruby-lang.org/en">Ruby</a><span>programming languages are provided.</span></p>
<p><span>http://genometools.org/annotationsketch.html</span></p><p>Address of the bookmark: <a href="http://genometools.org/annotationsketch.html" rel="nofollow">http://genometools.org/annotationsketch.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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