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<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/39383?offset=20</link>
	<atom:link href="https://bioinformaticsonline.com/related/39383?offset=20" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/37581/comparativegenomics-exercise2</guid>
	<pubDate>Wed, 22 Aug 2018 22:10:56 -0500</pubDate>
	<link>https://bioinformaticsonline.com/file/view/37581/comparativegenomics-exercise2</link>
	<title><![CDATA[ComparativeGenomics Exercise2]]></title>
	<description><![CDATA[<p>COMPARATIVE MICROBIAL GENOMICS ANALYSIS WORKSHOP&nbsp; @&nbsp;cbs.dtu.dk</p><p>Free Bioinformatics workbench https://www.mn.uio.no/ifi/english/research/networks/clsi/earlier_seminars/2012/tammivesth_osloseminarfinal.pdf</p>]]></description>
	<dc:creator>Neel</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/37581" length="139956" type="application/pdf" />
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/42903/katherine-belov-lab</guid>
  <pubDate>Sun, 21 Feb 2021 22:59:35 -0600</pubDate>
  <link></link>
  <title><![CDATA[Katherine Belov Lab]]></title>
  <description><![CDATA[
<p>Evolution of the adaptive immune system Marsupial and monotreme immune genes MHC Diversity and Conservation Marsupial and monotreme genomics Comparative Genomics Genetics of Tasmanian Devil facial tumour disease</p>

<p>More at https://www.sydney.edu.au/science/about/our-people/academic-staff/kathy-belov.html</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43791/comparative-genomics-visualisation-tools</guid>
	<pubDate>Thu, 17 Feb 2022 05:37:55 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43791/comparative-genomics-visualisation-tools</link>
	<title><![CDATA[Comparative genomics visualisation tools !]]></title>
	<description><![CDATA[<p>Comparative genomics visualisation tools !</p><p>Address of the bookmark: <a href="https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&amp;selected=%23BRIG&amp;tag=Comparative" rel="nofollow">https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&amp;selected=%23BRIG&amp;tag=Comparative</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34485/phyloxml-xml-for-evolutionary-biology-and-comparative-genomics</guid>
	<pubDate>Wed, 29 Nov 2017 10:04:48 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34485/phyloxml-xml-for-evolutionary-biology-and-comparative-genomics</link>
	<title><![CDATA[phyloXML:  XML for evolutionary biology and comparative genomics]]></title>
	<description><![CDATA[<p><a href="http://www.biomedcentral.com/1471-2105/10/356/">phyloXML</a><span>&nbsp;(</span><a href="http://www.phyloxml.org/examples_syntax/phyloxml_syntax_example_1.html">example</a><span>) is an&nbsp;</span><a href="http://en.wikipedia.org/wiki/XML">XML</a><span>&nbsp;language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly used features, such as taxonomic information, gene names and identifiers, branch lengths, support values, and gene duplication and speciation events. Using these standardized elements allows interoperability between various applications and databases. Furthermore, both due to extensible nature of XML itself and the provision of &lt;property&gt; elements by phyloXML, extensibility as well as domain specific applications are ensured. The structure of phyloXML is described by&nbsp;</span><a href="http://en.wikipedia.org/wiki/XML_Schema_%28W3C%29">XML Schema Definition (XSD)</a><span>&nbsp;language.</span></p><p>Address of the bookmark: <a href="http://www.phyloxml.org/" rel="nofollow">http://www.phyloxml.org/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36954/mscaffolder-a-comparative-genome-scaffolding-tool</guid>
	<pubDate>Fri, 15 Jun 2018 04:48:01 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36954/mscaffolder-a-comparative-genome-scaffolding-tool</link>
	<title><![CDATA[mScaffolder: A comparative genome scaffolding tool]]></title>
	<description><![CDATA[<p>A comparative genome scaffolding tool based on MUMmer</p>
<p>mScaffolder scaffolds a genome using an existing high quality genome as the reference. It aligns the two genomes using nucmer utility from MUMmer and then orders and orients the contigs of the candidate genome guided by their alignments to the reference genome. Please send your questions and comments to&nbsp;<a href="mailto:mchakrab@uci.edu">mchakrab@uci.edu</a>.</p>
<p><span>Citation</span><span>&nbsp;</span><a href="https://www.nature.com/articles/s41588-017-0010-y">https://www.nature.com/articles/s41588-017-0010-y</a></p><p>Address of the bookmark: <a href="https://github.com/mahulchak/mscaffolder" rel="nofollow">https://github.com/mahulchak/mscaffolder</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40476/libsdyogen-libibrary-for-comparative-genomics</guid>
	<pubDate>Wed, 25 Dec 2019 01:32:39 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40476/libsdyogen-libibrary-for-comparative-genomics</link>
	<title><![CDATA[LibsDyogen: Libibrary for comparative genomics]]></title>
	<description><![CDATA[<p>Library of usual classes and functions written in python and used in the Dyogen team for comparative genomics applications.</p>
<p>Collaborative python library used in the<span>&nbsp;</span><a href="http://www.ibens.ens.fr/?rubrique43&amp;lang=fr">DYOGEN team</a>for studying the evolution of gene order in vertebrates.</p>
<p><a href="http://www.ibens.ens.fr/?rubrique43&amp;lang=fr">http://www.ibens.ens.fr/?rubrique43&amp;lang=fr</a></p>
<p>&nbsp;</p><p>Address of the bookmark: <a href="https://github.com/DyogenIBENS/LibsDyogen" rel="nofollow">https://github.com/DyogenIBENS/LibsDyogen</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/43928/bioinformaticians-in-comparative-and-evolutionary-genomics</guid>
  <pubDate>Tue, 02 Aug 2022 01:22:48 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformaticians in comparative and evolutionary genomics]]></title>
  <description><![CDATA[
<p>NBIS is now looking for a new member to support Swedish research in evolutionary, comparative, and population genomics, with a particular focus on conifer genomics.</p>

<p>Your tasks will consist of:</p>

<p>Advanced bioinformatics analyses within research projects across Sweden, including key involvement in a major research effort in conifer genomics.<br />Development of bioinformatics tools and workflows.<br />Educating other scientists in bioinformatics through collaboration within supported projects, teaching at national courses, and through participating in various networks.<br />Taking part in the continuous development of NBIS/SciLifeLab at a national level</p>

<p>More at https://www.uu.se/en/about-uu/join-us/details/?positionId=518909</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources</guid>
	<pubDate>Tue, 28 Jun 2022 04:08:06 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources</link>
	<title><![CDATA[List of comparative genomics resources !]]></title>
	<description><![CDATA[<div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1096638041"><span>3D-GENOMICS -- A Database to Compare Structural and Functional Annotations of Proteins between Sequenced Genomes</span></a></div><p>Compare structural and functional annotations of proteins between sequenced genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1100640374"><span>ARED Organism -- expansion of ARED reveals AU-rich element cluster variations between human and mouse</span></a></div><p>View AREs in the human transcriptome and study the comparative genomics of AREs in model organisms.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1234973128"><span>ATGC -- Alignable Tight Genomic Clusters Database</span></a></div><p>Find information about orthologous genes in prokaryotes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1174596104"><span>AnimalQTLdb -- a livestock QTL database tool set for positional QTL information mining and beyond</span></a></div><p>Search for publicly available QTL data on livestocks and animal species.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL20110518150135"><span>BGDB -- Bovine Genome Database</span></a></div><p>Find information about bovine genomics data.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1229012662"><span>COMPARE -- a multi-organism system for cross-species data comparison and transfer of information</span></a></div><p>A multi-organism web-based resource system designed to easily retrieve, correlate and interpret data across species.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1218141952"><span>CONDOR -- COnserved Non-coDing Orthologous Regions</span></a></div><p>A database resource of developmentally associated conserved non-coding elements.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1099057221"><span>CORG -- A database for COmparative Regulatory Genomics</span></a></div><p>Delineate conserved non-coding blocks from upstream regions of putative orthologous gene pairs from man, mouse, rat, fugu, Mus musculus, Danio rerio, and zebrafish.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1203608896"><span>COXPRESdb -- a database of coexpressed gene networks in mammals</span></a></div><p>Find coexpressed gene lists and networks in human and mouse.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1097763045"><span>CVTree -- A Phylogenetic Tree Reconstruction Tool Based on Whole Genomes</span></a></div><p>Construct phylogenetic tree of microorganisms based on oligopeptide content of their complete proteomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1232729680"><span>CleanEST -- the cleansed EST libraries database</span></a></div><p>A novel database server that classifies GenBank's dbEST (database of expressed gene sequences) libraries and removes contaminants.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1256926144"><span>CoCoa -- COefficient of COAncestry software</span></a></div><p>Find information about the ancestral relationship between genes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1227549154"><span>CoGemiR -- a comparative genomics microRNA database</span></a></div><p>Provides an overview of the genomic organization of microRNAs and extent of conservation during evolution in different metazoan species.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1117678221"><span>Comparative Genometrics (CG) -- a database dedicated to biometric comparisons of whole genomes</span></a></div><p>Conduct comparative biometric analysis of chromosomes of different organisms.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1151007916"><span>DoTS -- Database Of Transcribed Sequences</span></a></div><p>Search for Indices of gene and transcripts in human and mouse.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1174510065"><span>DroSpeGe -- rapid access database for new Drosophila species genomes</span></a></div><p>Search and compare 12 new and old Drosophila genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1098208414"><span>ECR Browser -- A Tool for Visualizing and Accessing Data from Comparisons of Multiple Vertebrate Genomes</span></a></div><p>Access to whole genome alignments of human, mouse, rat and fish sequences.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1209738459"><span>EPGD -- Eukaryotic Paralog Group Database</span></a></div><p>Find eukaryotic paralog/paralogon information.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1232726869"><span>EVOG -- evolutionary visualizer for overlapping genes</span></a></div><p>Analyze the evolutionary process of overlapping genes when comparing different species.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1227633714"><span>GNAT -- Inter-species gene mention normalization (ISGN)</span></a></div><p>The first publicly available system reported to handle inter-species gene mention normalization.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1229438992"><span>GenColors -- annotation and comparative genomics of prokaryotes made easy</span></a></div><p>A web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1151086258"><span>GeneNest gene indices</span></a></div><p>Visualize gene indices of human, mouse, Arabidopsis, Zebrafish, Drosophila and Sheep.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1174489378"><span>GenomeTrafac -- a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs</span></a></div><p>Use comparative genomics approach to characterize gene models and identify putative cis-regulatory regions of RefSeq Gene Orthologs.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL20110518150753"><span>IKMC -- International Knockout Mouse Consortium web portal</span></a></div><p>Find information about mutated mouse genes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1209411604"><span>IMG/M -- Integrated Microbial Genomes/Metagenomes</span></a></div><p>A data management and analysis system for metagenomes</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1234976694"><span>ISED -- Influenza sequence and epitope database.</span></a></div><p>Search for influenza sequence, vaccine, and drug resistance information.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL20140710115515"><span>LAMDHI: The Search for Animal Models Starts Here</span></a></div><p>LAMHDI, the initiative to Link Animal Models to Human DIsease, is designed to accelerate the research process by providing biomedical researchers with a simple, comprehensive Web-based resource to find the best animal models for their research.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1228843803"><span>MANTIS -- a phylogenetic framework for multi-species genome comparisons</span></a></div><p>The missing link between multi-species full genome comparisons and functional analysis.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1099578148"><span>MBGD -- Microbial genome database for comparative analysis</span></a></div><p>Conduct comparative analysis of completely sequenced microbial genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1221077729"><span>MEGA -- Molecular Evolutionary Genetics Analysis</span></a></div><p>A biologist-centric software for evolutionary analysis of DNA and protein sequences.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1174596756"><span>MamPol -- a database of nucleotide polymorphism in the Mammalia class</span></a></div><p>Conduct single nucleotide polymorphisms diversity measurements among homologous sequences from the Mammalia class.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1266437314"><span>MicrobesOnline -- Prokaryotic Genome Database</span></a></div><p>Find information about 1000s of microbial genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1208461006"><span>Narcisse -- a mirror view of conserved syntenies</span></a></div><p>A database dedicated to the study of genome conservation.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1219772764"><span>OMA -- the Orthologous MAtrix project</span></a></div><p>Explore orthologous relations across 352 complete genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1209738741"><span>OPTIC -- orthologous and paralogous transcripts in clades</span></a></div><p>Browse complete genomes in several clades.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1209573208"><span>OrthoDB -- the hierarchical catalog of eukaryotic orthologs</span></a></div><p>Find groups of orthologous genes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1221231200"><span>OrthoMaM -- orthologous mammalian markers</span></a></div><p>A database of orthologous genomic markers for placental mammal phylogenetics.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1100009979"><span>PEDANT -- Protein Extraction, Description and ANalysis Tool</span></a></div><p>Conduct genome wide functional and structural analysis.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1174489475"><span>PReMod -- a database of genome-wide mammalian cis-regulatory module predictions</span></a></div><p>Conduct genome-wide cis-regulatory module (CRM) predictions for both the human and the mouse genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1151083092"><span>PhenomicDB -- Comparison of phenotypes of orthologous genes in human and model organisms</span></a></div><p>Compare phenotypes of a given gene or gene set in different model organisms.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1190899370"><span>Phylemon -- A suite of web tools for molecular evolution, phylogenetics and phylogenomics</span></a></div><p>Phylemon is a web server that integrates a selected suite of more than 20 different tools from the most popular stand-alone programs of phylogenetic and evolutionary analysis.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1232555615"><span>PhyloPat -- the phylogenetic pattern database</span></a></div><p>Use this database to see where in the evolution some phylogenetic lineages were started, and over which species they were contained.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1174510223"><span>Pristionchus.org -- a genome-centric database of the nematode satellite species Pristionchus pacificus</span></a></div><p>Search for genomic information on nematode satellite species Pristionchus pacificus.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1236367352"><span>ProtClustDB -- NCBI Protein Clusters Database</span></a></div><p>Find information about related protein sequences.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1209410278"><span>ProtozoaDB -- database of protozoan genomes</span></a></div><p>Database hosting genomics and post-genomics data from multiple protozoans.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1232554690"><span>Pseudofam -- the pseudogene families database</span></a></div><p>A database of pseudogene families based on the protein families from the Pfam database.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL20110518151439"><span>RIDM - RIKEN Integrated Database of Mammals</span></a></div><p>Find genomic information about mammals.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1272562567"><span>RegPrecise -- Regulon Prediction Database</span></a></div><p>Find information about predicted regulons in prokaryotic transcription regulation.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1272477473"><span>SALAD -- Surveyed contained motif ALignment diagram and the Associating Dendrogram</span></a></div><p>Perform systematic comparison of proteome data among species.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1229010765"><span>SGN -- SOL Genomics Network</span></a></div><p>A comparative map viewer dedicated to the biology of the Solanaceae family.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1256669040"><span>ShotgunFunctionalizeR -- R-package for functional comparison of metagenomes</span></a></div><p>Analyze data from functional analysis on fragmented microbial genetic material.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1256238439"><span>SnoopCGH -- Comparative Genomic Hybridization software</span></a></div><p>Visualize and explore comparative genomic hybridization data sets.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1174489598"><span>SwissRegulon -- a database of genome-wide annotations of regulatory sites</span></a></div><p>Search for genome-wide annotations of regulatory sites in yeast and prokaryotes genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1229013521"><span>TaxonGap -- a visualization tool for intra- and inter-species variation among individual biomarkers</span></a></div><p>Compare and select individual biomarkers.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1106063477"><span>The Adaptive Evolution Database (TAED) -- a phylogeny based tool for comparative genomics</span></a></div><p>Search for information on adaptive evolution in gene families of higher plants and chordate.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1216742716"><span>The CGView Server -- a comparative genomics tool for circular genomes</span></a></div><p>Generate graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1099663588"><span>The ERGO -- Genome analysis and discovery system</span></a></div><p>Conduct a comprehensive analysis of genes and genomes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1177611772"><span>The Macaque Genome: Interactive Poster and Teaching Resource</span></a></div><p>An interactive online poster presentation on the Macaque genome, including high-quality images, video clips, and Web resources</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1103816940"><span>The TIGR Gene Indices -- clustering and assembling EST and known genes and integration with eukaryotic genomes</span></a></div><p>Search for annotated genetic information of expressed sequence tags (ESTs) in different eukaryotic organisms.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1043767169"><span>UniGene</span></a></div><p>Find mapping and expression information for a unigene cluster (ESTs and full-length mRNA sequences organized into clusters that each represent a unique known or putative gene)</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1216738072"><span>Uprobe -- universal overgo hybridization-based probe retrieval and design</span></a></div><p>A public online resource for identifying or designing 'universal' overgo-hybridization probes from conserved sequences that can be used to efficiently screen one or more genomic libraries from a designated group of species.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1098205291"><span>VISTA -- Computational Tools for Comparative Genomics</span></a></div><p>Comprehensive suite of programs and databases for comparative analysis of genomic sequences.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL20110518144404"><span>cBARBEL -- Catfish Breeder and Researcher Bioinformatics Entry Location</span></a></div><p>Find information about ictalurid catfish.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1209738040"><span>eggNOG -- evolutionary genealogy of genes: Non-supervised Orthologous Groups</span></a></div><p>Discover orthologous groups of genes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1234370319"><span>metaTIGER -- a metabolic gene evolution resource</span></a></div><p>Find metabolic networks and phylogenomic information on a taxonomically diverse range of eukaryotes.</p></div><div><div><a href="https://www.hsls.pitt.edu/obrc/index.php?page=URL1138901833"><span>xBASE -- a collection of online databases for bacterial comparative genomics</span></a></div><p>Conduct bacterial comparative genomics.</p></div>]]></description>
	<dc:creator>Shruti Paniwala</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/news/view/13226/you-and-your-friend-have-similar-dna</guid>
	<pubDate>Sun, 27 Jul 2014 20:44:05 -0500</pubDate>
	<link>https://bioinformaticsonline.com/news/view/13226/you-and-your-friend-have-similar-dna</link>
	<title><![CDATA[You and your friend have similar DNA !!!]]></title>
	<description><![CDATA[<p>New research out of Massachusetts claims that people often choose friends that are similar to them in genetics and they are more accurate than you might suppose. A study published on PNAS&nbsp;http://www.pnas.org/content/111/Supplement_3/10796.full found that people are apt to pick friends who are genetically similar to themselves - so much so that friends tend to be as alike at the genetic level as a person's fourth cousin.</p><div style="text-align: center;"><img src="http://i.kinja-img.com/gawker-media/image/upload/s--CwLwHa43--/18fbmlokxcmqcjpg.jpg" alt="image" width="300" height="271" style="border: 0px; border: 0px;"></div><p>Scientists with a long-running Framingham Heart Study looked at 1,932 people (examination of about 1.5 million markers of genetic variations), comparing unrelated friends to unrelated strangers. They found that friends shared about 1% of their genes &mdash; a percentage much higher than those shared with strangers.This new findings made it clear that people have more DNA in common with those who are selected as friends than with strangers in the same population.&nbsp;</p><p>The genes that lined up the most were olfactory genes, which deal with smell. The ones that lined up the least were immune system genes. The researchers weren't sure why that happened :/. Olfactory genes might be a straightforward explanation: People who like the same smells tend to be drawn to similar environments, where they meet others with the same tendencies.</p><p>Reference:</p><p>http://www.pnas.org/content/111/Supplement_3/10796.full</p><p>Image : http://i.kinja-img.com</p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41222/best-practices-for-variant-calling-with-the-gatk</guid>
	<pubDate>Sat, 22 Feb 2020 03:07:31 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41222/best-practices-for-variant-calling-with-the-gatk</link>
	<title><![CDATA[Best Practices for Variant Calling with the GATK]]></title>
	<description><![CDATA[<p>The presentations below were filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. At the time of this workshop, the current version of Broad&rsquo;s Genome Analysis Toolkit (GATK) was version 3.3.</p>
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<li><a href="https://software.broadinstitute.org/gatk/">Genome Analysis Toolkit</a></li>
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<td>03/19/15</td>
<td>Introduction to High-Throughput Sequencing data formats and methods</td>
<td>Joel Thibault</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeY3g1M1ZjVjFrZ2s/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6696">Video</a></td>
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<td>03/19/15</td>
<td>Introduction to the GATK</td>
<td>Geraldine Van der Auwera</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeVEJ1Z1pXUF9Ib3M/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6707">Video</a></td>
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<td>03/19/15</td>
<td>Mapping, processing, and duplicate marking with Picard tools</td>
<td>Matt Sooknah</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeaGVrbE1GVV9SQkE/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6706">Video</a></td>
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<td>03/19/15</td>
<td>Mapping and processing RNAseq</td>
<td>Ami Levy-Moonshine</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeLUkwUm5vTGl4bG8/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6705">Video</a></td>
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<td>03/19/15</td>
<td>Indel realignment</td>
<td>Mark Fleharty</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeLTFzNndsNDBuVms/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6704">Video</a></td>
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<td>03/19/15</td>
<td>Base quality score recalibration</td>
<td>David Roazen</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeZk1rMXpTYmZzTXc/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6703">Video</a></td>
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<td>03/19/15</td>
<td>Introduction to variant discovery: calling cohorts</td>
<td>Louis Bergelson</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeQUFYUFRmM1hhRUE/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6702">Video</a></td>
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<td>03/19/15</td>
<td>Variant calling and joint genotyping</td>
<td>Sheila Chandran</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeYzVTUGs0bjM3M1E/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6701">Video</a></td>
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<td>03/19/15</td>
<td>Variant quality score recalibration</td>
<td>Bertrand Haas</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeSEpwRkNVQm4wdkE/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6700">Video</a></td>
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<td>03/19/15</td>
<td>Introduction to working with variants</td>
<td>Yossi Farjoun</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWec0NqUTN2WTRuWWs/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6699">Video</a></td>
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<td>03/19/15</td>
<td>Genotype refinement</td>
<td>Laura Gauthier</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeMzFldVF5SUp4dWM/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6698">Video</a></td>
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<td>03/19/15</td>
<td>Annotation and variant evaluation</td>
<td>David Benjamin</td>
<td><a href="https://docs.google.com/file/d/0B2dK2q40HDWeWi1YMm42bWdpRE0/preview" target="_blank">PDF</a></td>
<td><a href="https://www.broadinstitute.org/node/6697">Video</a></td>
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</table><p>Address of the bookmark: <a href="https://www.broadinstitute.org/partnerships/education/broade/best-practices-variant-calling-gatk-1" rel="nofollow">https://www.broadinstitute.org/partnerships/education/broade/best-practices-variant-calling-gatk-1</a></p>]]></description>
	<dc:creator>biogeek</dc:creator>
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