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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

UCSC Archaeal genome browserAdvanced browsing

September 19, 2006

David Bernick, Aaron Cozen and Todd Lowe

agenda
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
ucsc archaeal genome browser table browser
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

ucsc archaeal genome browser custom tracks
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
ucsc genome browser
UCSC Genome Browser
  • Advanced features:
    • Table Browser
    • Custom tracks
    • Conservation track and inter-species navigation