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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/44227?offset=10</link>
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	<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/41493/coronavirus-resources</guid>
	<pubDate>Wed, 25 Mar 2020 17:11:33 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41493/coronavirus-resources</link>
	<title><![CDATA[Coronavirus Resources !]]></title>
	<description><![CDATA[<p><span>2019nCoVR features comprehensive integration of genomic and proteomic sequences as well as their metadata information from the GISAID, NCBI, NMDC and CNCB/NGDC. It also incorporates a wide range of relevant information including scientific literatures, news, and popular articles for science dissemination, and provides visualization functionalities for genome variation analysis results based on all collected 2019-nCoV strains.</span></p>
<p><span>Annotation</span></p>
<p><span><a href="https://bigd.big.ac.cn/ncov/variation/annotation">https://bigd.big.ac.cn/ncov/variation/annotation</a></span></p>
<p><span>Genome wharehouse&nbsp;</span></p>
<p><span><a href="https://bigd.big.ac.cn/gwh/browse/index">https://bigd.big.ac.cn/gwh/browse/index</a></span></p>
<p>Released Genome</p>
<p><a href="https://bigd.big.ac.cn/ncov/release_genome">https://bigd.big.ac.cn/ncov/release_genome</a></p>
<p>Download data&nbsp;</p>
<p><a href="ftp://download.big.ac.cn/Genome/Viruses/Coronaviridae/">ftp://download.big.ac.cn/Genome/Viruses/Coronaviridae/</a></p>
<p>Raw data</p>
<p><a href="https://bigd.big.ac.cn/gsa/browse/run/?tag=Coronaviridae">https://bigd.big.ac.cn/gsa/browse/run/?tag=Coronaviridae</a></p><p>Address of the bookmark: <a href="https://bigd.big.ac.cn/ncov/about" rel="nofollow">https://bigd.big.ac.cn/ncov/about</a></p>]]></description>
	<dc:creator>Neel</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/36905/d-genies-a-tool-for-dotplot-large-genomes-in-an-interactive-efficient-and-simple-way</guid>
	<pubDate>Mon, 11 Jun 2018 09:41:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36905/d-genies-a-tool-for-dotplot-large-genomes-in-an-interactive-efficient-and-simple-way</link>
	<title><![CDATA[D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way]]></title>
	<description><![CDATA[D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation.

We use minimap version 2 to align the two genomes. Then, the PAF file is parsed and plotted into an interactive plot written with d3.js library.

D-Genies also allows to display dot plots from other aligners by uploading their PAF or MAF alignment file.

http://dgenies.toulouse.inra.fr/<p>Address of the bookmark: <a href="http://dgenies.toulouse.inra.fr/" rel="nofollow">http://dgenies.toulouse.inra.fr/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39872/miropeats-discovers-regions-of-sequence-similarity-amongst-any-set-of-dna-sequences</guid>
	<pubDate>Mon, 26 Aug 2019 17:55:24 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39872/miropeats-discovers-regions-of-sequence-similarity-amongst-any-set-of-dna-sequences</link>
	<title><![CDATA[Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences]]></title>
	<description><![CDATA[<p><span>Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then presents this similarity information graphically. Sequence similarity searching is a very general tool that forms the basis of many different biological sequence analyses but it is limited by the verbosity of traditional alignment presentation styles. Miropeats enhances the utility of conventional DNA sequence comparisons when looking at long lengths of sequence similarity by summarizing extensive large scale sequence similarities on a single page of graphics. The latest version of Miropeats can be used as a general pairwise alignment program or in its traditional role sorting out a big mess of overlapping or similar regions.</span></p><p>Address of the bookmark: <a href="http://www.littlest.co.uk/software/bioinf/old_packages/miropeats/" rel="nofollow">http://www.littlest.co.uk/software/bioinf/old_packages/miropeats/</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42359/dnasp-dna-sequence-polymorphism-is-a-software-package-for-the-analysis-of-dna-polymorphisms</guid>
	<pubDate>Wed, 25 Nov 2020 19:51:38 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42359/dnasp-dna-sequence-polymorphism-is-a-software-package-for-the-analysis-of-dna-polymorphisms</link>
	<title><![CDATA[DnaSP: DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms]]></title>
	<description><![CDATA[<p><span>DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms using data from a single locus (a multiple sequence aligned -MSA data), or from several loci (a Multiple-MSA data, such as formats generated by some assembler RAD-seq software). DnaSP can estimate several measures of DNA sequence variation within and between populations in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters.</span></p><p>Address of the bookmark: <a href="http://www.ub.edu/dnasp/" rel="nofollow">http://www.ub.edu/dnasp/</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38670/ltr-finder-an-efficient-program-for-finding-full-length-ltr-retrotranspsons-in-genome-sequences</guid>
	<pubDate>Sun, 13 Jan 2019 07:05:53 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38670/ltr-finder-an-efficient-program-for-finding-full-length-ltr-retrotranspsons-in-genome-sequences</link>
	<title><![CDATA[LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.]]></title>
	<description><![CDATA[<p>LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.</p>
<p>The Program first constructs all exact match pairs by a suffix-array based algorithm and extends them to long highly similar pairs. Then Smith-Waterman algorithm is used to adjust the ends of LTR pair candidates to get alignment boundaries. These boundaries are subject to re-adjustment using supporting information of TG..CA box and TSRs and reliable LTRs are selected. Next, LTR_FINDER tries to identify PBS, PPT and RT inside LTR pairs by build-in aligning and counting modules. RT identification includes a dynamic programming to process frame shift. For other protein domains, LTR_FINDER calls ps_scan (from PROSITE,&nbsp;<a href="http://www.expasy.org/prosite/">http://www.expasy.org/prosite/</a>) to locate cores of important enzymes if they occur.</p><p>Address of the bookmark: <a href="https://github.com/xzhub/LTR_Finder" rel="nofollow">https://github.com/xzhub/LTR_Finder</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<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>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/2423/cancers-origins-revealed</guid>
	<pubDate>Thu, 15 Aug 2013 13:06:56 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/2423/cancers-origins-revealed</link>
	<title><![CDATA[Cancer's origins revealed]]></title>
	<description><![CDATA[<p>Researchers have provided the first comprehensive compendium of mutational processes that drive tumour development. Together, these mutational processes explain most mutations found in 30 of the most common cancer types. This new understanding of cancer development could help to treat and prevent a wide-range of cancers.<br /><br />More at &gt;&gt; http://www.sanger.ac.uk/about/press/2013/130814.html</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/3918/the-human-genome-project-video-3d-animation-introduction-low</guid>
	<pubDate>Sat, 24 Aug 2013 19:01:19 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/3918/the-human-genome-project-video-3d-animation-introduction-low</link>
	<title><![CDATA[The Human Genome Project Video   3D Animation Introduction Low)]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/YxoQFSBwyms" frameborder="0" allowfullscreen></iframe>]]></description>
	
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