1. 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

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  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 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

4. Table browser 2 set up query

5. Table browser 3

6. 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

7. Custom tracks

8. Custom tracks - examples

9. Custom tracks - example 2 WIGgle tracks

10. Conservation track

11. 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