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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/26325?offset=1180</link>
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	<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/researchlabs/view/44650/manthey-research-group-%E2%80%93-evolutionary-genomics</guid>
  <pubDate>Thu, 22 Aug 2024 06:25:55 -0500</pubDate>
  <link></link>
  <title><![CDATA[Manthey Research Group – Evolutionary Genomics]]></title>
  <description><![CDATA[
<p>We focus on fundamental questions in genomics, ecology, and evolution. Our methods include fieldwork and labwork, but most of our time is spent analyzing genomics data using computational biology approaches.</p>

<p>Ant / bacteria co-evolution, landscape genomics, and population genomics<br />Vertebrate and/or invertebrate genome evolution</p>

<p>If you might be interested in joining our research group, send an email with your intent and why this group would potentially be a good fit for your future goals along with a CV / Resume to jdmanthey (at) gmail (dot) com</p>

<p>More at https://mantheylab.org/</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44770/nvidia-and-arc-institute-unveil-evo-2-a-breakthrough-ai-for-dna-design</guid>
	<pubDate>Fri, 21 Feb 2025 10:39:47 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44770/nvidia-and-arc-institute-unveil-evo-2-a-breakthrough-ai-for-dna-design</link>
	<title><![CDATA[NVIDIA and Arc Institute Unveil Evo 2: A Breakthrough AI for DNA Design]]></title>
	<description><![CDATA[<p>NVIDIA and the Arc Institute have introduced <strong style="font-size: 12.8px;">Evo 2</strong>, a groundbreaking AI model designed to <strong style="font-size: 12.8px;">understand, predict, and generate DNA sequences</strong>. This marks a major advancement in computational biology, offering scientists an unprecedented tool to decode the genetic blueprint of life and even design entirely new biological systems.</p><h3><strong>The Power of Evo 2: AI Meets DNA</strong></h3><p>Evo 2 is <strong>the largest AI model for biology ever created</strong>, trained on an astonishing <strong>9.3 trillion DNA "letters"</strong> (nucleotides) carefully selected from genomes spanning the entire tree of life. This massive dataset ensures that Evo 2 can recognize patterns and relationships in genetic sequences at an unparalleled scale.</p><p>For the first time, scientists can <strong>design DNA with AI</strong>, moving beyond simple sequence analysis to active DNA generation. Evo 2 enables researchers to <strong>predict, modify, and even create entire genetic sequences</strong>, opening new possibilities in medicine, agriculture, and synthetic biology.</p><h3><strong>Decoding the Dark Genome</strong></h3><p>One of the biggest challenges in genetics is understanding the <strong>non-coding regions</strong> of DNA&mdash;vast stretches of the genome that do not code for proteins but play crucial roles in regulating gene expression. These regions control when and how genes are activated, influencing everything from development to disease.</p><p>Evo 2 is designed to <strong>decode these non-coding elements</strong>, helping researchers uncover their functions and use this knowledge to develop gene-based therapies, synthetic life forms, and precision agriculture solutions.</p><h3><strong>From Reading DNA to Writing It</strong></h3><p>To put Evo 2&rsquo;s impact into perspective:</p><ul>
<li><strong>Previous AI models could "read" DNA</strong> like a book, analyzing genetic sequences and identifying patterns.</li>
<li><strong>Evo 2 can "write" entirely new DNA</strong>, designing functional genes, chromosomes, and even full genomes from scratch.</li>
</ul><p>This means scientists can now <strong>engineer biological systems with AI</strong>, designing new proteins, metabolic pathways, and genetic circuits to address real-world challenges.</p><h3><strong>A Step Toward Generative Biology</strong></h3><p>The Arc Institute describes Evo 2 as a major step toward <strong>"generative biology"</strong>&mdash;a revolutionary approach where AI is used to create <strong>novel biological structures</strong> rather than just analyzing existing ones. This could lead to breakthroughs such as:</p><ul>
<li><strong>New medicines</strong>: AI-generated enzymes and proteins tailored for targeted therapies.</li>
<li><strong>Disease-resistant crops</strong>: Genetically optimized plants for higher yield and climate resilience.</li>
<li><strong>Synthetic organisms</strong>: Custom-designed microbes for bioremediation, biofuel production, and industrial applications.</li>
</ul><h3><strong>An Open-Source Revolution</strong></h3><p>Unlike many proprietary AI models, <strong>Evo 2 is open source</strong>, making its capabilities accessible to researchers worldwide. This democratization of AI-driven biology means that scientists from different disciplines can <strong>collaborate, experiment, and innovate</strong>, accelerating discoveries in genetic engineering and synthetic biology.</p><p>With Evo 2, the boundaries of what&rsquo;s possible in <strong>DNA design, genetic engineering, and biological innovation</strong> are being redrawn. The future of life sciences is no longer just about understanding life&rsquo;s code&mdash;it&rsquo;s about writing it.</p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34549/kraken-a-universal-genomic-coordinate-translator-for-comparative-genomics</guid>
	<pubDate>Thu, 07 Dec 2017 04:45:43 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34549/kraken-a-universal-genomic-coordinate-translator-for-comparative-genomics</link>
	<title><![CDATA[kraken: A universal genomic coordinate translator for comparative genomics]]></title>
	<description><![CDATA[<p><span>If you planning on conducting a study involving dozens of large genomes, then you do not have to run all pairwise synteny alignments .. simply try&nbsp;kraken: A universal genomic coordinate translator for comparative genomics</span></p><p>Address of the bookmark: <a href="https://github.com/nedaz/kraken" rel="nofollow">https://github.com/nedaz/kraken</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38006/scribl-html5-canvas-genomics-graphic-library</guid>
	<pubDate>Thu, 25 Oct 2018 09:38:53 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38006/scribl-html5-canvas-genomics-graphic-library</link>
	<title><![CDATA[Scribl : HTML5 canvas genomics graphic library]]></title>
	<description><![CDATA[<p>Scribl is a javascript, Canvas-based graphics library that easily generates biological visuals of genomic regions, alignments, and assembly data. Scribl can also be used in conventional offline pipelines, since everything needed to generate charts can be contained in a single html file.</p>
<p>&nbsp;</p><p>Address of the bookmark: <a href="http://chmille4.github.io/Scribl/" rel="nofollow">http://chmille4.github.io/Scribl/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40369/phyloxml-xml-for-evolutionary-biology-and-comparative-genomics</guid>
	<pubDate>Sun, 08 Dec 2019 09:41:18 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40369/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><a href="http://www.phyloxml.org/archaeopteryx-js/adh.html">http://www.phyloxml.org/archaeopteryx-js/adh.html</a></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/42143/sibelia-a-comparative-genomics-tool</guid>
	<pubDate>Sat, 22 Aug 2020 02:49:00 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42143/sibelia-a-comparative-genomics-tool</link>
	<title><![CDATA[Sibelia: A comparative genomics tool]]></title>
	<description><![CDATA[<p><strong>Sibelia</strong>: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms.&nbsp;</p>
<p><strong>Sibelia</strong>&nbsp;is useful in finding: (1) shared regions, (2) regions that present in one group of genomes but not in others, (3) rearrangements that transform one genome to other genomes.</p>
<p>More at&nbsp;<a href="http://bioinf.spbau.ru/sibelia">http://bioinf.spbau.ru/sibelia</a></p>
<p>Sibelia docs&nbsp;<a href="http://gensoft.pasteur.fr/docs/Sibelia/3.0.7/SIBELIA.md">http://gensoft.pasteur.fr/docs/Sibelia/3.0.7/SIBELIA.md</a></p><p>Address of the bookmark: <a href="https://github.com/bioinf/Sibelia" rel="nofollow">https://github.com/bioinf/Sibelia</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44661/lovis4u-locus-visualisation-tool-for-comparative-genomics</guid>
	<pubDate>Tue, 17 Sep 2024 02:30:57 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44661/lovis4u-locus-visualisation-tool-for-comparative-genomics</link>
	<title><![CDATA[LoVis4u: Locus Visualisation tool for comparative genomics]]></title>
	<description><![CDATA[<p dir="auto"><a href="https://github.com/art-egorov/lovis4u/blob/main/docs/img/lovis4u_logo.png" target="_blank"><img src="https://github.com/art-egorov/lovis4u/raw/main/docs/img/lovis4u_logo.png" alt="image" width="300" style="border: 0px; border: 0px;"></a></p>
<div dir="auto">
<h2 dir="auto">Description</h2>
<a href="https://github.com/art-egorov/lovis4u#description"></a></div>
<p dir="auto"><span>LoVis4u</span>&nbsp;is a bioinformatics tool for&nbsp;<span>Lo</span>ci&nbsp;<span>Vis</span>ualisation.</p>
<p dir="auto"><span>LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualisation of multiple genomic loci. LoVis4u generates vector images in PDF format based on annotation data from GenBank or GFF files. It is capable of visualising entire genomes of bacteriophages as well as plasmids and user-defined regions of longer prokaryotic genomes. Additionally, LoVis4u offers optional data processing steps to identify and highlight accessory and core genes in input sequences.</span></p>
<p dir="auto">https://art-egorov.github.io/lovis4u/</p>
<p dir="auto">&nbsp;</p><p>Address of the bookmark: <a href="https://github.com/art-egorov/lovis4u" rel="nofollow">https://github.com/art-egorov/lovis4u</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/11107/the-minerva-research-group-for-bioinformatics</guid>
  <pubDate>Tue, 27 May 2014 15:48:14 -0500</pubDate>
  <link></link>
  <title><![CDATA[The Minerva Research Group for Bioinformatics]]></title>
  <description><![CDATA[
<p>The focus of the bioinformatics group is to use computational approaches to gain an insight into genome evolution in primates.</p>

<p>http://www.eva.mpg.de/genetics/bioinformatics/overview.html?Fsize=0%2C%20%40%2F%27</p>

<p>Kelso Group<br />Department of Evolutionary Genetics<br />Max Planck Institute for Evolutionary Anthropology<br />Deutscher Platz 6<br />04103 Leipzig<br />Germany<br />Phone: +49 341 3550 500</p>

<p>Job: <br />http://www.eva.mpg.de/genetics/bioinformatics/jobs.html?Fsize=0%2C%2B%40</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/11175/next-generation-sequencingngs-books</guid>
	<pubDate>Fri, 30 May 2014 04:48:04 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/11175/next-generation-sequencingngs-books</link>
	<title><![CDATA[Next generation sequencing(NGS) books]]></title>
	<description><![CDATA[<p>Employing different technologies, the purpose of NGS platform is to decode the identity or modification on the nucleotides. NGS platforms evolve quickly and capture the main stream.</p>
<p>This bookmark is created to provide NGS online books links.</p><p>Address of the bookmark: <a href="http://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Print_version" rel="nofollow">http://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Print_version</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
</item>

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