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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/32154?offset=160</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44472/pipesnake-bioinformatics-best-practice-analysis-pipeline-for-phylogenomic-reconstruction</guid>
	<pubDate>Wed, 21 Feb 2024 06:19:41 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44472/pipesnake-bioinformatics-best-practice-analysis-pipeline-for-phylogenomic-reconstruction</link>
	<title><![CDATA[pipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction]]></title>
	<description><![CDATA[<p dir="auto"><span>ausarg/pipesnake</span>&nbsp;is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.</p>
<p dir="auto">The pipeline is built using&nbsp;<a href="https://www.nextflow.io/">Nextflow</a>, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The&nbsp;<a href="https://www.nextflow.io/docs/latest/dsl2.html">Nextflow DSL2</a>&nbsp;implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.</p><p>Address of the bookmark: <a href="https://github.com/AusARG/pipesnake" rel="nofollow">https://github.com/AusARG/pipesnake</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41969/shadowcaster-a-hybrid-approach-for-the-detection-of-horizontal-gene-transfer-events-in-prokaryotes</guid>
	<pubDate>Tue, 14 Jul 2020 06:42:10 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41969/shadowcaster-a-hybrid-approach-for-the-detection-of-horizontal-gene-transfer-events-in-prokaryotes</link>
	<title><![CDATA[ShadowCaster: a hybrid approach for the detection of horizontal gene transfer events in prokaryotes]]></title>
	<description><![CDATA[<p><span>ShadowCaster implements an evolutionary model to calculate Bayesian likelihoods for each &lsquo;alien genes&rsquo; with an unusual sequence composition according to the host genome background to detect HGT events in prokaryotes.</span></p>
<p><a href="https://www.mdpi.com/2073-4425/11/7/756/htm">https://www.mdpi.com/2073-4425/11/7/756/htm</a></p>
<p><a href="https://shadowcaster.readthedocs.io/en/latest/">https://shadowcaster.readthedocs.io/en/latest/</a></p>
<p><a href="https://github.com/dani2s/ShadowCaster_testData">https://github.com/dani2s/ShadowCaster_testData</a></p><p>Address of the bookmark: <a href="https://github.com/dani2s/ShadowCaster" rel="nofollow">https://github.com/dani2s/ShadowCaster</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44902/hite-a-fast-and-accurate-dynamic-boundary-adjustment-approach-for-full-length-transposable-elements-detection-and-annotation-in-genome-assemblies</guid>
	<pubDate>Sat, 20 Sep 2025 09:34:04 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44902/hite-a-fast-and-accurate-dynamic-boundary-adjustment-approach-for-full-length-transposable-elements-detection-and-annotation-in-genome-assemblies</link>
	<title><![CDATA[HiTE: a fast and accurate dynamic boundary adjustment approach for full-length Transposable Elements detection and annotation in Genome Assemblies]]></title>
	<description><![CDATA[<p dir="auto"><code>HiTE</code>&nbsp;is a Python software that uses a dynamic boundary adjustment approach to detect and annotate full-length Transposable Elements in Genome Assemblies. In comparison to other tools, HiTE demonstrates superior performance in detecting a greater number of full-length TEs.</p>
<div dir="auto">
<h2 dir="auto">panHiTE</h2>
<a href="https://github.com/CSU-KangHu/HiTE#panhite"></a></div>
<p dir="auto">We have developed panHiTE, a comprehensive and accurate pipeline for TE detection in large-scale population genomes. It has been successfully applied to hundreds of plant population genomes, demonstrating its effectiveness and scalability.</p>
<p dir="auto">For detailed instructions, please refer to the&nbsp;<a href="https://github.com/CSU-KangHu/HiTE/wiki/panHiTE-tutorial">panHiTE tutorial</a>.</p><p>Address of the bookmark: <a href="https://github.com/CSU-KangHu/HiTE" rel="nofollow">https://github.com/CSU-KangHu/HiTE</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/11249/how-to-sequence-the-human-genome-mark-j-kiel</guid>
	<pubDate>Fri, 30 May 2014 13:24:11 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/11249/how-to-sequence-the-human-genome-mark-j-kiel</link>
	<title><![CDATA[How to sequence the human genome - Mark J. Kiel]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/MvuYATh7Y74" frameborder="0" allowfullscreen></iframe>View full lesson: http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel

Your genome, every human's genome, consists of a unique DNA sequence of A's, T's, C's and G's that tell your cells how to operate. Thanks to technological advances, scientists are now able to know the sequence of letters that makes up an individual genome relatively quickly and inexpensively. Mark J. Kiel takes an in-depth look at the science behind the sequence.

Lesson by Mark J. Kiel, animation by Marc Christoforidis.]]></description>
	
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/12870/nuclear-dynamics-lab</guid>
  <pubDate>Thu, 17 Jul 2014 15:03:27 -0500</pubDate>
  <link></link>
  <title><![CDATA[Nuclear Dynamics Lab]]></title>
  <description><![CDATA[
<p>Lab focus is to elucidate fundamental principles, new mechanisms, machineries and emergent properties that are involved in maintaining the genome and gene expression programmes for improvements in lifelong health and well-being for all.</p>

<p>More at http://www.babraham.ac.uk/our-research/nuclear-dynamics/</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43867/genomeqc-a-quality-assessment-tool-for-genome-assemblies-and-gene-structure-annotations</guid>
	<pubDate>Thu, 19 May 2022 04:29:05 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43867/genomeqc-a-quality-assessment-tool-for-genome-assemblies-and-gene-structure-annotations</link>
	<title><![CDATA[GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations]]></title>
	<description><![CDATA[<p><span>The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at&nbsp;</span><a href="https://genomeqc.maizegdb.org/">https://genomeqc.maizegdb.org/</a><span>&nbsp;under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository&nbsp;</span><a href="https://github.com/HuffordLab/GenomeQC">https://github.com/HuffordLab/GenomeQC</a><span>.</span></p>
<p>https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-6568-2</p><p>Address of the bookmark: <a href="https://github.com/HuffordLab/GenomeQC" rel="nofollow">https://github.com/HuffordLab/GenomeQC</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/14800/a-comprehensive-atlas-of-human-gene-activity-released</guid>
	<pubDate>Tue, 02 Sep 2014 14:20:24 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/14800/a-comprehensive-atlas-of-human-gene-activity-released</link>
	<title><![CDATA[A comprehensive atlas of human gene activity released !!!]]></title>
	<description><![CDATA[<div><div id="postDescription_4018558404"><p>A large international consortium of researchers has produced the first comprehensive, detailed map of the way&nbsp;<a href="http://www.hsph.harvard.edu/news/topic/genetics/" target="_blank">genes</a>&nbsp;work across the major cells and tissues of the human body. The findings describe the complex networks that govern gene activity, and the new information could play a crucial role in identifying the genes involved with disease.</p><p><img src="http://www.kurzweilai.net/images/Coexpression-clustering.jpg" alt="image" width="640" height="460" style="border: 0px; border: 0px;"></p><p>We are able to pinpoint the regions of the genome that can be active in a disease and in normal activity, whether it&rsquo;s in a brain cell, the skin, in blood stem cells or in hair follicles. This is a major advance that will greatly increase our ability to understand the causes of disease across the body.</p><p>The research is outlined in a series of papers published March 27, 2014, two in the journal&nbsp;<em>Nature</em>&nbsp;and 16 in other scholarly journals. The work is the result of years of concerted effort among 250 experts from more than 20 countries as part of&nbsp;<a href="http://fantom.gsc.riken.jp/" target="_blank">FANTOM 5 (Functional Annotation of the Mammalian Genome)</a>. The FANTOM project, led by the Japanese institution RIKEN, is aimed at building a complete library of human genes.</p><p>Researchers studied human and mouse cells using a new technology called Cap Analysis of Gene Expression (CAGE), developed at RIKEN, to discover how 95% of all human genes are switched on and off. These &ldquo;switches&rdquo; &mdash; called &ldquo;promoters&rdquo; and &ldquo;enhancers&rdquo; &mdash; are the regions of DNA that manage gene activity. The researchers mapped the activity of 180,000 promoters and 44,000 enhancers across a wide range of human cell types and tissues and, in most cases, found they were linked with specific cell types.</p><p>Referene : www.kurzweilai.net/first-comprehensive-atlas-of-human-gene-activity-released</p></div></div>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37211/jbrowse-embeddable-genome-browser-built-completely-with-javascript-and-html5</guid>
	<pubDate>Fri, 29 Jun 2018 09:19:56 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37211/jbrowse-embeddable-genome-browser-built-completely-with-javascript-and-html5</link>
	<title><![CDATA[JBrowse: Embeddable genome browser built completely with JavaScript and HTML5]]></title>
	<description><![CDATA[JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl.

Headline Features:
Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed.
Scales easily to multi-gigabase genomes and deep-coverage sequencing.
Quickly open and view data files on your computer without uploading them to any server.
Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with either .tbi or .idx index), REST, and more.  BAM, BigBed, BigWig, and VCF data are displayed directly from chunks of the compressed binary files, no conversion needed.
Includes an optional “faceted” track selector (see demo) suitable for large installations with thousands of tracks.
Very light server resource requirements. In fact, JBrowse has no back-end server code, just tools for formatting data files to be read directly over HTTP. Serve huge datasets from a single low-cost cloud instance.
Can run as a stand-alone app on OSX and Windows using the Electron platform
Highly extensible plugin architecture, with a large plugin registry of existing examples here https://gmod.github.io/jbrowse-registry

https://jbrowse.org/<p>Address of the bookmark: <a href="https://github.com/GMOD/jbrowse" rel="nofollow">https://github.com/GMOD/jbrowse</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/19090/deeptools</guid>
	<pubDate>Sat, 08 Nov 2014 15:02:08 -0600</pubDate>
	<link>https://bioinformaticsonline.com/news/view/19090/deeptools</link>
	<title><![CDATA[deepTools]]></title>
	<description><![CDATA[<p>deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. To do so, deepTools contains useful modules to process the mapped reads data to create coverage files in standard bedGraph and bigWig file formats. By doing so, deepTools allows the creation of normalized coverage files or the comparison between two files (for example, treatment and control). Finally, using such normalized and standardized files, multiple visualizations can be created to identify enrichments with functional annotations of the genome.<br /><br />Publicaton: http://nar.oxfordjournals.org/content/early/2014/05/05/nar.gku365.full<br /><br />Source Code and Wiki: https://github.com/fidelram/deepTools/wiki<br /><br />Galaxy Tool Shed repository: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools<br /><br />and example Galaxy workflows: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_workflows</p>]]></description>
	<dc:creator>Martin Jones</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40465/airlift-a-methodology-and-tool-for-comprehensively-moving-mappings-and-annotations-from-one-genome-to-another-similar-genome</guid>
	<pubDate>Mon, 23 Dec 2019 10:20:13 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40465/airlift-a-methodology-and-tool-for-comprehensively-moving-mappings-and-annotations-from-one-genome-to-another-similar-genome</link>
	<title><![CDATA[AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome]]></title>
	<description><![CDATA[<p>We propose AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome while maintaining the accuracy of a full mapper.</p><p>Address of the bookmark: <a href="https://github.com/CMU-SAFARI/AirLift" rel="nofollow">https://github.com/CMU-SAFARI/AirLift</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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