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UCSC Archaeal genome browser Advanced browsing

UCSC Archaeal genome browser Advanced browsing. September 19, 2006 David Bernick , Aaron Cozen and Todd Lowe. Agenda. Basic searches with the Archaea Genome browser Text searches Sequence searching - BLAT, short sequences In-silico PCR Hands-on session - Navigation and searching

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UCSC Archaeal genome browser Advanced browsing

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  1. UCSC Archaeal genome browserAdvanced browsing September 19, 2006 David Bernick, Aaron Cozen and Todd Lowe

  2. Agenda • Basic searches with the Archaea Genome browser • Text searches • Sequence searching - BLAT, short sequences • In-silico PCR • Hands-on session - Navigation and searching • Advanced features • Table Browser • Custom tracks • Conservation tracks and inter-species navigation • Hands-on session - Table Browser and Custom tracks

  3. UCSC Archaeal Genome BrowserTable browser Typically used for text based queries For example: Which tRNA genes in Pyrococcus furiosus have an overlap with an annotated protein coding region? 2 step query: select all Refseq annotated coding regions intersect this group with tRNA annotated regions

  4. Table browser 2set up query

  5. Table browser 3

  6. UCSC Archaeal Genome BrowserCustom tracks • Allows addition of your data within the browser • Supports compressed or uncompressed files, using • Tab separated data in GFF, GTF, BED or WIG formats • BED files support disjoint data • WIG files support continuous valued data

  7. Custom tracks

  8. Custom tracks - examples

  9. Custom tracks - example 2WIGgle tracks

  10. Conservation track

  11. UCSC Genome Browser • Advanced features: • Table Browser • Custom tracks • Conservation track and inter-species navigation

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