7 research outputs found
Multiple whole genome alignments and novel biomedical applications at the VISTA portal
The VISTA portal for comparative genomics is designed to give biomedical scientists a unified set of tools to lead them from the raw DNA sequences through the alignment and annotation to the visualization of the results. The VISTA portal also hosts the alignments of a number of genomes computed by our group, allowing users to study the regions of their interest without having to manually download the individual sequences. Here we describe various algorithmic and functional improvements implemented in the VISTA portal over the last 2 years. The VISTA Portal is accessible at http://genome.lbl.gov/vista
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Comparative Genomics Tools for analysis of Six Dothideomycete Genomes
Comparative genomics is a powerful tool for genome annotation and analysis. We recently initiated analysis of six of the Dothideomycete genomes that are publicly available: Mycosphaerella graminicola, Mycosphaerella fijiensis and Cochliobolus heterostropus C5 all sequenced and annotated at the DOE Joint Genome Institute as well as Alternaria brassicicola sequenced at the Washington University School of Medicine, Genome Sequencing Center and annotated by the Christopher Lawrence Lab at Virginia Bioinformatics Institute, Virginia Tech, Pyrenophora tritici-repentis and Stagonospora nodorum, both sequenced and annotated by the Broad Institute, MIT. We placed these genomes into a comparative framework equipped with tools to facilitate genome analysis: VISTA genome conservation curves linking genome browsers, gene cluster browser and protein links to homologs in all six genomes, side-by-side comparisons of KEGG pathways and KOG functions, and synteny viewer. JGI community annotation brought biologists behind each of these genomes together to explore common mechanisms of plant pathogenicity and host interactions
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The VISTA Synteny Viewer: Navigating Whole Genome Alignments at Multiple Levels of Resolution
Comparison of whole-genome assemblies is required at all stages of their completion and analysis ? from individual reads to draft and finished genomes, from assembly through finishing and annotation. We have expanded the VISTA suite of tools for comparative genomics by adding a novel interactive web application, the VISTA Synteny Viewer (VSV), for the navigation of whole genome alignments at multiple levels of resolution. The VSV uses modern web technologies to tightly wed the visualization of DNA synteny at the level of whole genomes, individual chromosomes/scaffolds, and individual aligned loci, as well to dynamically generate dot plots
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The VISTA Synteny Viewer: Navigating Whole Genome Alignments at Multiple Levels of Resolution
Comparison of whole-genome assemblies is required at all stages of their completion and analysis ? from individual reads to draft and finished genomes, from assembly through finishing and annotation. We have expanded the VISTA suite of tools for comparative genomics by adding a novel interactive web application, the VISTA Synteny Viewer (VSV), for the navigation of whole genome alignments at multiple levels of resolution. The VSV uses modern web technologies to tightly wed the visualization of DNA synteny at the level of whole genomes, individual chromosomes/scaffolds, and individual aligned loci, as well to dynamically generate dot plots