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Paul Bain Reference and Education Services Librarian Countway Library of Medicine

Genome Browsers. Paul Bain Reference and Education Services Librarian Countway Library of Medicine pbain@hms.harvard.edu 617-432-3236 Countway Reference and Education Services 617-432-2134. Genome Browsers. Genetic and molecular data organized and coordinated with whole genomic sequences

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Paul Bain Reference and Education Services Librarian Countway Library of Medicine

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  1. Genome Browsers Paul Bain Reference and Education Services LibrarianCountway Library of Medicine pbain@hms.harvard.edu617-432-3236 Countway Reference and Education Services617-432-2134 Bootcamp: Data Resources

  2. Genome Browsers • Genetic and molecular data organized and coordinated with whole genomic sequences • A good source of data! Provide both graphical and bulk access • Annotations from diverse sources • Can include gene prediction and structure, proteins, expression, regulation, variation, comparative analysis and much more • Facilitate comparative analysis Bootcamp: Data Resources

  3. Genome Browsers • UCSC Genome Browser genome.ucsc.edu • Ensembl Genome Browser ensembl.org uswest.ensembl.org • NCBI MapViewer www.ncbi.nih.gov/mapview Bootcamp: Data Resources

  4. Other Genome Browsers • MGI Mouse Genome Informatics - JAX • GBrowse The GMOD GBrowse Project • Integrated Microbial Genomes (IMG) system by the DOE-Joint Genome Institute • Pathway Tools Genome Browser • X:Map A genome browser that shows Affymetrix Exon Microarray hit locations alongside the gene, transcript and exon data on a Google maps api • Viral Genome Organizer (VGO) A genome browser providing visualization and analysis tools for annotated whole genomes from the eleven virus families in the VBRC (Viral Bioinformatics Resource Center) databases • Apollo Genome Annotation Curation Tool A cross-platform, JAVA-based standalone genome viewer with enterprise-level functionality and customizations. The standard for many model organism databases. • SEED viewer for visualizing and interrogating the SEED database of complete microbial genomes • Integrated Genome Browser (IGB) A cross-platform, Java-based desktop genome viewer. • Argo Genome Browser A free and open source standalone Java-based genome browser for visualizing and manually annotating whole genomes. • UGENE A free, cross-platform and high-performance genome browser integrated with multiple view and analysis tools. Bootcamp: Data Resources

  5. UCSC Genome Browser • About 20 Vertebrate genomesalso insects, squirts, and nematodes • Very fast • BLAT for both protein and nucleotide • Large number of annotations, comparative genomics • Useful secondary tools, e.g. Gene Sorter, VisiGene • ENCODE data • Supported by HHMI, NHGRI Bootcamp: Data Resources

  6. Ensembl • 58 Eukaryotic Genomes • Graphically pleasing with easy to read maps • SSAHA, and now BLAT for nucleotide sequences • Very large collection of annotations • Superior linking of data • BioMart • Supported by EMBL-EBI, Wellcome Trust Sanger Institute Bootcamp: Data Resources

  7. Getting Help • Each browser has its own help resources • Countway/MIT videos for UCSCBITS: www.countway.harvard.edu/video_tutorials • Reading: Nucleic Acids Research Database Issue (Open Access)nar.oxfordjournals.org/Latest (2010, Vol. 38, Suppl. 1): nar.oxfordjournals.org/content/vol38/suppl_1/index.dtl Current Protocols in Bioinformatics (Baxevanis, A.D, et al. eds., New York : Wiley)nrs.harvard.edu/urn-3:HUL.ejournals:sfx1000000000390431 Bootcamp: Data Resources

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