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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/36607?offset=320</link>
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	<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/26911/raca-reference-assisted-chromosome-assembly</guid>
	<pubDate>Wed, 06 Apr 2016 09:29:50 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26911/raca-reference-assisted-chromosome-assembly</link>
	<title><![CDATA[RACA: Reference-Assisted Chromosome Assembly]]></title>
	<description><![CDATA[<p>Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads.</p>
<p>http://www.ncbi.nlm.nih.gov/pubmed/23307812</p>
<p>http://bioen-compbio.bioen.illinois.edu/RACA/</p><p>Address of the bookmark: <a href="http://bioen-compbio.bioen.illinois.edu/RACA/" rel="nofollow">http://bioen-compbio.bioen.illinois.edu/RACA/</a></p>]]></description>
	<dc:creator>Priya Singh</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/27080/mrfast-micro-read-fast-alignment-search-tool</guid>
	<pubDate>Tue, 26 Apr 2016 03:50:06 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27080/mrfast-micro-read-fast-alignment-search-tool</link>
	<title><![CDATA[mrFAST:  Micro Read Fast Alignment Search Tool]]></title>
	<description><![CDATA[<p><span>mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 4+4 bp. This manual, describes how to choose the parameters and tune mrFAST with respect to the library settings. mrFAST is designed to find&nbsp;</span><strong><span style="text-decoration: underline;">'all'</span></strong><span>&nbsp; mappings for a given set of reads, however it can return one "best" map location if the relevant parameter is invoked.</span></p>
<p><span>More at&nbsp;http://mrfast.sourceforge.net/manual.html</span></p><p>Address of the bookmark: <a href="http://mrfast.sourceforge.net/manual.html" rel="nofollow">http://mrfast.sourceforge.net/manual.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/29614/art-set-of-simulation-tools</guid>
	<pubDate>Thu, 03 Nov 2016 08:28:25 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29614/art-set-of-simulation-tools</link>
	<title><![CDATA[ART: Set of Simulation Tools]]></title>
	<description><![CDATA[<p>ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and Applied Biosystems' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART was used as a primary tool for the simulation study of the <span><a href="http://www.1000genomes.org/" target="_blank">1000 Genomes Project<span></span></a></span> . ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format. ART can be used together with genome variants simulators (e.g. <span><a href="http://bioinform.github.io/varsim/" target="_blank">VarSim<span></span></a></span>) for evaluating variant calling tools or methods.</p><p>Address of the bookmark: <a href="http://www.niehs.nih.gov/research/resources/software/biostatistics/art/" rel="nofollow">http://www.niehs.nih.gov/research/resources/software/biostatistics/art/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30557/speedseq</guid>
	<pubDate>Fri, 20 Jan 2017 06:05:43 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30557/speedseq</link>
	<title><![CDATA[SpeedSeq]]></title>
	<description><![CDATA[<p>A flexible framework for rapid genome analysis and interpretation</p>
<p>C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth (2015). doi:10.1038/nmeth.3505.</p>
<p><a href="http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html">http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html</a></p><p>Address of the bookmark: <a href="https://github.com/hall-lab/speedseq" rel="nofollow">https://github.com/hall-lab/speedseq</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/31568/pacbio-long-reads-compatible-software-and-tools</guid>
	<pubDate>Wed, 15 Mar 2017 14:19:01 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/31568/pacbio-long-reads-compatible-software-and-tools</link>
	<title><![CDATA[Pacbio Long Reads Compatible Software and Tools]]></title>
	<description><![CDATA[<p>The following software packages are known to be compatible with PacBio&reg; data, in addition to PacBio's own SMRT&reg; Analysis suite. All packages are believed to be open source or freely available for non-commercial use. See the individual project sites for up-to-date license information. A separate page lists&nbsp;<a href="http://pacb.com/community/partner_program/current_partners/">commercial software</a>.</p>
<p>Know of any other open source software for PacBio data?&nbsp;<a href="mailto:devnet@pacificbiosciences.com">Email us</a>.</p>
<p>Software categories:</p>
<ul>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#denovo">De novo assembly</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#svdetection">Structural Variations Detection</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#aligners">Reference-based alignment</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#variants">Consensus and variant calling</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#RNA">RNA analysis</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#basemods">Epigenetic base modifications and methylation</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#barcoding">Barcoding</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#browsers">Genome Browsers</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#qc">Run QC</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#frameworks">Frameworks and APIs</a></li>
</ul><p>Address of the bookmark: <a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software" rel="nofollow">https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software</a></p>]]></description>
	<dc:creator>Archana Malhotra</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40940/consed-a-finishing-package-bam-file-viewer-assembly-editor-autofinish-autoreport-autoedit-and-align-reads-to-reference-sequence</guid>
	<pubDate>Fri, 07 Feb 2020 07:16:22 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40940/consed-a-finishing-package-bam-file-viewer-assembly-editor-autofinish-autoreport-autoedit-and-align-reads-to-reference-sequence</link>
	<title><![CDATA[Consed--A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)]]></title>
	<description><![CDATA[<ul>
<li>Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types</li>
<li>Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence in targeted regions.</li>
<li>Consed is compatible with Newbler, Cross_match, Phrap, MIRA, Velvet and PCAP output.</li>
<li>Quickly takes the user to each variant site for viewing (also available as an automated report)</li>
<li>Overview of assembly can help detect and fix misassemblies</li>
<li>Editing time reduced by the program's ability to pin-point problem areas</li>
<li>Editing is guided by error probabilities</li>
</ul><p>Address of the bookmark: <a href="http://www.phrap.org/consed/consed.html" rel="nofollow">http://www.phrap.org/consed/consed.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44593/bear-better-emulation-for-artificial-reads</guid>
	<pubDate>Sat, 06 Jul 2024 04:27:53 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44593/bear-better-emulation-for-artificial-reads</link>
	<title><![CDATA[BEAR: Better Emulation for Artificial Reads]]></title>
	<description><![CDATA[<p dir="auto">Created by Stephen Johnson, Brett Trost, Dr. Jeffrey R. Long, Dr. Anthony Kusalik University of Saskatchewan, Department of Computer Science</p>
<p dir="auto">BEAR is intended to be an easy-to-use collection of scripts for generating simulated WGS metagenomic reads with read lengths, quality scores, error profiles, and species abundances derived from real user-supplied WGS data.</p><p>Address of the bookmark: <a href="https://github.com/sej917/BEAR" rel="nofollow">https://github.com/sej917/BEAR</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36746/soap2-short-oligonucleotide-analysis-package-2</guid>
	<pubDate>Wed, 23 May 2018 10:09:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36746/soap2-short-oligonucleotide-analysis-package-2</link>
	<title><![CDATA[SOAP2 : Short Oligonucleotide Analysis Package 2]]></title>
	<description><![CDATA[SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order of magnitude faster. It require only 2 minutes aligning one million single-end reads onto the human reference genome. Another remarkable improvement of SOAPaligner is that it now supports a wide range of the read length.

SOAPaligner benefitted in time and space efficiency by a revolution in the basic data structures and algorithms used.The core algorithms and the indexing data structures (2way-BWT) are developed by the algorithms research group of the Department of Computer Science, the University of Hong Kong (T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu).<p>Address of the bookmark: <a href="http://soap.genomics.org.cn/soapaligner.html" rel="nofollow">http://soap.genomics.org.cn/soapaligner.html</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/27110/easyfig</guid>
	<pubDate>Fri, 29 Apr 2016 05:49:39 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27110/easyfig</link>
	<title><![CDATA[Easyfig]]></title>
	<description><![CDATA[<p>Easyfig has moved to github, for newer releases of Easyfig please visit our new webpage - https://mjsull.github.io/Easyfig.&nbsp; Easyfig is a Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).</p>
<p>More at http://easyfig.sourceforge.net/</p><p>Address of the bookmark: <a href="http://easyfig.sourceforge.net/" rel="nofollow">http://easyfig.sourceforge.net/</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
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