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Practically Genomic … A hands-on Bioinformatics IAP - Genome Analysis

Practically Genomic … A hands-on Bioinformatics IAP - Genome Analysis. The Structure of Genomic Data Annotating Genomic Sequence With Argo The UCSC Genome Browser and Database Basic Searches BLAT Searches Custom Tracks Table Browser Gene Sorter Proteome Browser Other Genomics Resources.

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Practically Genomic … A hands-on Bioinformatics IAP - Genome Analysis

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  1. Practically Genomic…A hands-on Bioinformatics IAP - Genome Analysis • The Structure of Genomic Data • Annotating Genomic Sequence With Argo • The UCSC Genome Browser and Database • Basic Searches • BLAT Searches • Custom Tracks • Table Browser • Gene Sorter • Proteome Browser • Other Genomics Resources

  2. The Structure of Genomic Data chr1 blast exon 349834 349975 96 + 0 genex • The above is gff format. There are many other similar formats. • All formats accomplish the same thing. • DNA name • Feature type • Start and Stop in chromosome • Strand • Name of feature

  3. Operations on Genomic Data • Annotation • The identification and labeling of genomic features • Genes, repeats, CpG islands, Conserved blocks etc. • Manual and automated approaches can be applied • Huge amounts of annotation has been done • Characterization of Relationships • How do the various annotated features relate to one another? • Overlaps, Non-Overlaps, Density, etc. • Usually accomplished with database queries. • The UCSC tools and Argo facilitate both of these operations

  4. Annotation - Argo • Genome browser and Annotation tool • Written by Reinhard Engles at the Broad Institute • Visualization and editing tools are Argo’s main strengths.

  5. Relationships - The UCSC Browser and Database navigate navigate General information Specific information— new features, current status, etc.

  6. The UCSC Genome Browser OpenHelix offers excellent training material UCSC Genome Browser Training Materials developed by: Warren C. Lathe, Ph.D. Mary Mangan, Ph.D. http://openhelix.com/index.shtml

  7. UCSC Genome Browser credits • http://genome.ucsc.edu/goldenPath/credits.html • Led by David Haussler and Jim Kent • Dozens of staff and students also work to bring you this software and data

  8. ENSEMBL - http://www.ensembl.org/index.html • Example for Training: http://www.ensembl.org/info/worked_example.pdf

  9. Broad Institute - http://www.broad.mit.edu/

  10. JGI - http://genome.jgi-psf.org/

  11. NCBI - http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi

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