1. UCSC Archaeal genome browser 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 http://archaea.ucsc.edu http://archaea.ucsc.edu UCSC Archaeal Genome Browser http://archaea.ucsc.edu http://archaea.ucsc.edu

4. UCSC Archaeal Genome Browser sample search for “regulatory proteins”

5. coordinates and annotated direction, using Genbank, Tigr and Rfam conservation predicted promoters and terminators

6. Short sequence searching

7. Short sequence input

9. Sequence searching - BLAT search with either nucleotide or protein sequence

11. BLAT results

12. BLAT result - detail

13. BLAT result - browser

14. BLAT search - multiple hits

15. BLAT- multiple hit response

16. BLAT - tRNA D arm

17. in-silico PCR primer search

18. in-silico search results

19. UCSC Genome Browser PCR Results -

20. UCSC Genome Browser review  Searching  Text annotation- name and description  Short sequence  Blat - protein or nucleotide sequence  in-silico PCR  Searching  Text annotation- name and description  Short sequence  Blat - protein or nucleotide sequence  in-silico PCR