Genome Browsers.

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Model Organism Databases and Community Annotation
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Presentation transcript:

Genome Browsers

Genome Browser Combines a genome database with interactive web pages Allows the user to retrieve and manipulate database record through a graphical user interface (GUI) Different types of information are displayed in an intuitive fashion in user-configurable “tracks”

GFF3 files are hard to interpret

MAKER genes & RNAseq reads in GBrowse

Genome Browsers for repeat definition Show is a track displaying the results of a genome “blasted” against itself

A plethora of genome browsers Annmap Apollo Genome Annotation Curation Tool Argo Genome Browser Avadis NGS BugView Celera Genome Browser Dalliance DiProGB DNAnexus Ensembl Gaggle Genome Browser GBrowse The Genomic HyperBrowser Genostar GenoBrowser GenPlay Integrated Genome Browser (IGB) Integrated Microbial Genomes (IMG) JBrowse (a JavaScript browser ) MGV - Microbial Genome Viewer MochiView Genome Browser NextBio Genome Browser Pathway Tools Genome Browser Savant Genome Browser SEED viewer UCSC Genome Bioinformatics Genome Browser Viral Genome Organizer (VGO) VISTA genome browser

Today’s activity Use the Integrated Genome Browser Populate the browser with data: A Magnaporthe sequence contig MAKER annotations Mapped RNAseq reads RNAseq read heatmaps Explore the browser to get an idea of how it works and how the tracks can be manipulated/activated/deactivated

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