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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/39213?offset=640</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42130/shaman-a-user-friendly-website-for-metataxonomic-analysis-from-raw-reads-to-statistical-analysis</guid>
	<pubDate>Mon, 17 Aug 2020 05:21:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42130/shaman-a-user-friendly-website-for-metataxonomic-analysis-from-raw-reads-to-statistical-analysis</link>
	<title><![CDATA[SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis]]></title>
	<description><![CDATA[<p><span>SHAMAN is a shiny application for differential analysis of metagenomic data (16S, 18S, 23S, 28S, ITS and WGS) including bioinformatics treatment of raw reads for targeted metagenomics, statistical analysis and results visualization with a large variety of plots (barplot, boxplot, heatmap, &hellip;).</span><br><span>The bioinformatics treatment is based on Vsearch [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/27781170">Rognes 2016</a><span>] which showed to be both accurate and fast [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/26664811">Wescott 2015</a><span>].The statistical analysis is based on DESeq2 R package [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/20979621">Anders and Huber 2010</a><span>] which robustly identifies the differential abundant features as suggested in [</span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974642/">McMurdie and Holmes 2014</a><span>] and [</span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727335/">Jonsson2016</a><span>]. SHAMAN robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/25516281">Love 2014</a><span>].</span><br><span>SHAMAN is compatible with standard formats for metagenomic analysis (.csv, .tsv, .biom) and figures can be downloaded in several formats. A presentation about SHAMAN is available&nbsp;</span><a href="https://github.com/aghozlane/shaman/blob/master/www/shaman_presentation.pdf">here</a><span>&nbsp;and a poster&nbsp;</span><a href="https://github.com/aghozlane/shaman/blob/master/www/shaman_poster.pdf">here</a><span>.&nbsp;</span></p>
<p><span>More at&nbsp;<a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03666-4">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03666-4</a></span></p><p>Address of the bookmark: <a href="https://github.com/aghozlane/shaman" rel="nofollow">https://github.com/aghozlane/shaman</a></p>]]></description>
	<dc:creator>BioStar</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/32129/lordec-a-hybrid-error-correction-program-for-long-pacbio-reads</guid>
	<pubDate>Mon, 10 Apr 2017 04:16:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/32129/lordec-a-hybrid-error-correction-program-for-long-pacbio-reads</link>
	<title><![CDATA[LoRDEC: a hybrid error correction program for long, PacBio reads]]></title>
	<description><![CDATA[<p>LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads. It uses a hybrid strategy, meaning that it uses two sets of reads: the reference read set, whose error rate is assumed to be small, and the PacBio read set, which is then corrected using the reference set. Typically, the reference set contains Illumina reads.</p>
<p><br> Usually, errors in PacBio reads include many insertions and deletions, and comparatively less substitutions. LoRDEC can correct errors of all these types.<br> After correction, a larger portion of the sequence of PacBio reads is usable for detection of region of similarity with other sequences, for aligning them to the contigs of an assembly, etc.</p>
<p>Why is LoRDEC different?</p>
<ul>
<li>It is efficient and can process large read data sets, included from eukaryotic or vertebrate species, on a usual computing server, and even works on desktop/laptop computers.</li>
<li>It adopts a novel graph based approach: it builds a succinct De Bruijn Graph (DBG) representing the short reads, and seeks a corrective sequence for each erroneous region of a long read by traversing chosen paths in the graph.</li>
</ul><p>Address of the bookmark: <a href="http://www.atgc-montpellier.fr/lordec/" rel="nofollow">http://www.atgc-montpellier.fr/lordec/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40893/quorum-an-error-corrector-for-illumina-reads</guid>
	<pubDate>Tue, 04 Feb 2020 23:26:55 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40893/quorum-an-error-corrector-for-illumina-reads</link>
	<title><![CDATA[QuorUM: An Error Corrector for Illumina Reads]]></title>
	<description><![CDATA[<p><span>We produce trimmed and error-corrected reads that result in assemblies with longer contigs and fewer errors. We compared QuorUM against several published error correctors and found that it is the best performer in most metrics we use. QuorUM is efficiently implemented making use of current multi-core computing architectures and it is suitable for large data sets (1 billion bases checked and corrected per day per core)</span></p><p>Address of the bookmark: <a href="http://www.genome.umd.edu/" rel="nofollow">http://www.genome.umd.edu/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/view/982</guid>
	<pubDate>Wed, 17 Jul 2013 15:25:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/view/982</link>
	<title><![CDATA[Is reference genome necessary for gene expression study in transcriptome sequencing or for variant discovery in genome sequencing?]]></title>
	<description><![CDATA[<p><span>Like in case of plant genomes where nature of genome is too complex and huge in size to accomplish complete<em> de novo</em> assembly by current sequencing technology. What would be alternate solution? Can we live in reference free world?</span></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/2518/genome-browsers</guid>
	<pubDate>Fri, 16 Aug 2013 19:04:47 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/2518/genome-browsers</link>
	<title><![CDATA[Genome Browsers]]></title>
	<description><![CDATA[<p>Genome Browser is the platform/database used for searching and retreiving sequences and annotation of genomes belong to various eukaryotes, prokaryotes, etc.</p><p>Following are the weblink for different available browsers:</p><p><a href="http://www.ensembl.org/index.html">http://www.ensembl.org/index.html</a></p><p><a href="http://ensemblgenomes.org/">http://ensemblgenomes.org/</a></p><p><a href="http://genome.ucsc.edu/">http://genome.ucsc.edu/</a></p><p><a href="http://www.ncbi.nlm.nih.gov/genome">http://www.ncbi.nlm.nih.gov/genome</a></p><p><a href="http://www.ebi.ac.uk/genomes/">http://www.ebi.ac.uk/genomes/</a></p><p><a href="http://flybase.org/">http://flybase.org/</a></p><p><a href="http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi">http://cmr.jcvi.org/tigr-scripts/CMR/CmrHomePage.cgi</a></p><p><a href="http://www.sanger.ac.uk/resources/databases/">http://www.sanger.ac.uk/resources/databases/</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/4208/latest-paper-on-comparison-of-mapping-tools</guid>
	<pubDate>Tue, 03 Sep 2013 18:00:38 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/4208/latest-paper-on-comparison-of-mapping-tools</link>
	<title><![CDATA[Latest paper on comparison of mapping tools]]></title>
	<description><![CDATA[<p>A. Hatem, D. Bozdag, A. E. Toland, U. V. Catalyurek "Benchmarking short sequence mapping tools" BMC Bioinformatics, 14(1):184, 2013.</p>
<p>http://bmi.osu.edu/hpc/software/benchmark/</p>
<p><a href="http://bmi.osu.edu/hpc/software/pmap/pmap.html">http://bmi.osu.edu/hpc/software/pmap/pmap.html</a></p>
<p>Other similiar papers:</p>
<p><a href="http://online.liebertpub.com/doi/pdf/10.1089/cmb.2012.0022">http://online.liebertpub.com/doi/pdf/10.1089/cmb.2012.0022</a></p>
<p><a href="http://bioinformatics.oxfordjournals.org/content/28/24/3169">http://bioinformatics.oxfordjournals.org/content/28/24/3169</a></p>
<p>Some new Mapping tool links:<a href="http://bmi.osu.edu/hpc/software/benchmark/"></a></p>
<p><strong>GSNAP</strong></p>
<p><a href="http://research-pub.gene.com/gmap/"></a><a href="http://research-pub.gene.com/gmap/">http://research-pub.gene.com/gmap/</a></p>
<p><strong>RMAP</strong></p>
<p><a href="http://rulai.cshl.edu/rmap/"></a><a href="http://rulai.cshl.edu/rmap/">http://rulai.cshl.edu/rmap/</a></p>
<p><strong>mrsFAST</strong></p>
<p><a href="http://mrsfast.sourceforge.net/Home"></a><a href="http://mrsfast.sourceforge.net/Home">http://mrsfast.sourceforge.net/Home</a></p>
<p><a href="http://sourceforge.net/projects/mrsfast/files/mrsfast-ultra-3.1.0/">http://sourceforge.net/projects/mrsfast/files/mrsfast-ultra-3.1.0/</a></p>
<p><strong>BFAST</strong></p>
<p><a href="http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page">http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page</a></p>
<p><strong>SHRiMP (for&nbsp;AB SOLiD color-space reads)</strong></p>
<p><a href="http://compbio.cs.toronto.edu/shrimp/">http://compbio.cs.toronto.edu/shrimp/</a></p>
<p><strong>RazerA 3</strong></p>
<p><a href="http://www.seqan.de/projects/razers/">http://www.seqan.de/projects/razers/</a></p><p>Address of the bookmark: <a href="http://www.biomedcentral.com/1471-2105/14/184" rel="nofollow">http://www.biomedcentral.com/1471-2105/14/184</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/9400/largest-genome-sequenced</guid>
	<pubDate>Fri, 21 Mar 2014 13:57:19 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/9400/largest-genome-sequenced</link>
	<title><![CDATA[Largest Genome Sequenced]]></title>
	<description><![CDATA[<p>The enormous size of the <strong>loblolly pine genome</strong> having <strong>22 billion base pairs</strong> compared to only 3 billion in the human genome. In other words, it is&nbsp;<strong>seven times</strong> larger than a human&rsquo;s and also the largest and the most complete&nbsp;<strong>conifer<a href="http://en.wikipedia.org/wiki/Pinophyta" target="_blank"></a></strong>&nbsp;genome ever sequenced.</p>
<p><strong>Related Paper:</strong></p>
<p>http://genomebiology.com/2014/15/3/R59/abstract</p>
<p>&nbsp;</p><p>Address of the bookmark: <a href="http://www.news.ucdavis.edu/search/news_detail.lasso?id=10859" rel="nofollow">http://www.news.ucdavis.edu/search/news_detail.lasso?id=10859</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/10243/new-rna-seq-tool</guid>
	<pubDate>Fri, 25 Apr 2014 10:59:04 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/10243/new-rna-seq-tool</link>
	<title><![CDATA[New RNA Seq tool]]></title>
	<description><![CDATA[<p>"<span>By removing the time-consuming step of read mapping, the authors reported, Sailfish able to provide quantification estimates 20&ndash;30 times faster than current methods without loss of accuracy."</span></p>
<p><span>Tool link:</span></p>
<p><span>http://www.cs.cmu.edu/~ckingsf/software/sailfish/</span></p>
<p><span></span></p><p>Address of the bookmark: <a href="http://www.genengnews.com/gen-news-highlights/lightweight-algorithms-sail-through-rna-sequencing-data/81249765/" rel="nofollow">http://www.genengnews.com/gen-news-highlights/lightweight-algorithms-sail-through-rna-sequencing-data/81249765/</a></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/10966/genxpro-gmbh</guid>
	<pubDate>Thu, 22 May 2014 07:18:35 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/10966/genxpro-gmbh</link>
	<title><![CDATA[GenXPro GmbH]]></title>
	<description><![CDATA[<p><strong>GenXPro</strong>&nbsp;GMbH is service provider for entire spectrum of nucleotide-based information&nbsp;of any biological sample. By combining intelligent data reduction techniques and&nbsp;latest next generation sequencing technologies, our service portfolio provides most accurate and cost efficient solutions for&nbsp;transcriptomic-, genomic- or epigenomic research.</p><p><span><span><strong><span>GENXPRO GMBH</span>,&nbsp;</strong></span></span><span>ALTENH&Ouml;FERALLEE 3,&nbsp;</span><span>60438 FRANKFURT MAIN,&nbsp;</span><span>GERMANY</span></p><p><span><span><strong>Website</strong></span>:&nbsp;<a href="http://www.genxpro.info/products_and_services/"></a><a href="http://www.genxpro.info/products_and_services/">http://www.genxpro.info/products_and_services/</a></span></p><p><span><strong>PHONE</strong>: +49 (0)69- 95 73 97 10,&nbsp;FAX: +49 (0)69- 95 73 97 06</span></p><p><span>EMAIL: info@genxpro.de</span></p>]]></description>
	<dc:creator>Rahul Agarwal</dc:creator>
</item>

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