UCSC Archaeal genome browser Advanced browsing September 19, 2006 David Bernick, Aaron Cozen and Todd Lowe 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 Advanced features Table Browser Custom tracks Conservation tracks and inter-species navigation Hands-on session - Table Browser and Custom tracks 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 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 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 3
UCSC Archaeal Genome Browser Custom 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 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 - examples
Custom tracks - example 2 WIGgle tracks
Conservation track
UCSC Genome Browser Advanced features: Table Browser Custom tracks Conservation track and inter-species navigation Advanced features: Table Browser Custom tracks Conservation track and inter-species navigation