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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/41602?offset=40</link>
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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>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40994/biological-databases</guid>
	<pubDate>Wed, 12 Feb 2020 01:16:29 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40994/biological-databases</link>
	<title><![CDATA[Biological databases !]]></title>
	<description><![CDATA[<p>Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ...</p>
<p>ftp://ftp.ncbi.nih.gov/genomes/</p>
<p>https://hgdownload.soe.ucsc.edu/downloads.html</p><p>Address of the bookmark: <a href="ftp://ftp.ncbi.nih.gov/genomes/" rel="nofollow">ftp://ftp.ncbi.nih.gov/genomes/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/26499/katju-lab</guid>
  <pubDate>Fri, 26 Feb 2016 03:25:32 -0600</pubDate>
  <link></link>
  <title><![CDATA[Katju Lab]]></title>
  <description><![CDATA[
<p>TheLab seek to understand the genetic factors contributing to genomic variation and phenotypic diversity.  To this end, we employ molecular and bioinformatic tools to study evolutionary processes at the level of populations, both experimental and natural, and genomes.  Our research interests encompass a wide range of topics, including the evolution of organellar and nuclear genomes, gene duplication and the origin of novel function, and the fitness and phenotypic consequences of mutation in evolution. For details regards ongoing projects, please see the Research page.</p>

<p>http://katjulab.com/research.html</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38310/sisrs-site-identification-from-short-read-sequences</guid>
	<pubDate>Wed, 28 Nov 2018 08:56:03 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38310/sisrs-site-identification-from-short-read-sequences</link>
	<title><![CDATA[SISRS: Site Identification from Short Read Sequences]]></title>
	<description><![CDATA[<p>Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads must have a fastq file extension.</p><p>Address of the bookmark: <a href="https://github.com/rachelss/SISRS" rel="nofollow">https://github.com/rachelss/SISRS</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43799/kast</guid>
	<pubDate>Wed, 23 Feb 2022 08:28:36 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43799/kast</link>
	<title><![CDATA[KAST]]></title>
	<description><![CDATA[<p><span>Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.</span></p><p>Address of the bookmark: <a href="https://github.com/martinjvickers/KAST" rel="nofollow">https://github.com/martinjvickers/KAST</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37751/kast-perform-alignment-free-k-tuple-frequency-comparisons-from-sequences</guid>
	<pubDate>Thu, 20 Sep 2018 08:56:35 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37751/kast-perform-alignment-free-k-tuple-frequency-comparisons-from-sequences</link>
	<title><![CDATA[KAST: Perform Alignment-free k-tuple frequency comparisons from sequences]]></title>
	<description><![CDATA[<p><span>Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.</span></p><p>Address of the bookmark: <a href="https://github.com/martinjvickers/KAST" rel="nofollow">https://github.com/martinjvickers/KAST</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<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>
<item>
	<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>
<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>
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