Bootcamp: Data Resources1 Paul Bain Reference and Education Services Librarian Countway Library of Medicine 617-432-3236 Countway.

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Presentation transcript:

Bootcamp: Data Resources1 Paul Bain Reference and Education Services Librarian Countway Library of Medicine Countway Reference and Education Services Genome Browsers

Bootcamp: Data Resources2 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 Resources3 UCSC Genome Browser genome.ucsc.edu Ensembl Genome Browser ensembl.org uswest.ensembl.org NCBI MapViewer Genome Browsers

Bootcamp: Data Resources4 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 Resources5 UCSC Genome Browser About 20 Vertebrate genomes also 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 Resources6 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 Resources7 Getting Help Each browser has its own help resources Countway/MIT videos for UCSC BITS : 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:sfx