Ucsc archaeal genome browser advanced browsing
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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


Table browser 2 set up query

Table browser 2set up query


Table browser 3

Table browser 3


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


Custom tracks

Custom tracks


Custom tracks examples

Custom tracks - examples


Custom tracks example 2 wiggle tracks

Custom tracks - example 2WIGgle tracks


Conservation track

Conservation track


Ucsc genome browser

UCSC Genome Browser

  • Advanced features:

    • Table Browser

    • Custom tracks

    • Conservation track and inter-species navigation


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