1. The Genome Genome Browser Training Materials developed by: Warren C. Lathe, Ph.D. and Mary Mangan, Ph.D. info@openhelix.com Part 2

2. Gene Sorter Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser Hands-on session for Basic Searches Gene Sorting search using the Gene Sorter Advanced searching using the Table Browser Custom Tracks Hands-on session for Sorter, Table Browser, and Custom Tracks

3. Gene Sorter From homepage select ‘Gene sorter’

4. Gene Sorter interface Sorts genes by several criteria

5. Choose genome Choose assembly Type in gene name or accession # Gene Sorter interface

6. Choose from 11 sorting options

7. Gene Sorter interface Configure display view

8. Gene Sorter interface Filter data by different criteria

9. Gene Sorter results

10. Obtain file of gene sequences or tab-delineated file of data

11. Table Browser Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser Hands-on session for Basic Searches Gene Sorting search using the Gene Sorter Advanced searching using the Table Browser Custom Tracks Hands-on session for Sorter, Table Browser, and Custom Tracks

12. The Table Browser Download sequence of all simple repeats of copy number more than 10 from a position on chromosome 4.

13. The Table Browser From the Genome Browser home page, select Table Browser

14. Table browser: choose genome Choose genome and assembly

15. Table browser: choose table to search Data tables are organized by group & annotation track.

16. Table browser: choose region to search Choose entire genome, ENCODE regions, enter a single position or alternatively paste or upload a file of positions.

17. Table browser: filter to refine search Filter is a form based sql query. Filters can be created for primary table and for related tables

18. Table browser: Output formats Get fields of table data

19. Table browser: Output formats Fasta file of sequence data

20. Table browser: Output formats GTF or BED formated file

21. Table browser: Output formats Custom track

22. Table browser: Obtaining output Output as file or in browser. Also, obtain statistics. Adding name creates file on desktop, leaving blank creates output in browser. (exception: custom track) Obtain a summary of specified data

23. Table browser: Output configuration

24. The Table Browser Find simple repeats (copy number > 10) within known genes and download the sequence.

25. Table browser: Intersecting data Intersect table with another table of data

26. Table browser: Intersecting data Filtered simple repeats Filtered simple repeats, intersected (overlapping) w/ known genes Obtaining summary shows how intersecting narrowed search

27. Table browser: Intersecting data

28. Table browser: Correlating data

29. Custom Tracks Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser Hands-on session for Basic Searches Gene Sorting search using the Gene Sorter Advanced Searching using the Table Browser Custom Tracks Hands-on session for Sorter, Table Browser and Custom Tracks

30. Custom Tracks Table Browser Searches User-generated Data Externally Generated Data

31. Custom Tracks: Table browser searches

33. Custom Tracks can be viewed in the Genome Browser

34. Custom Tracks: Table browser searches Custom tracks also are available for filtering and intersections on the Table Browser.

35. Intersecting previously created custom track finds one simple repeat with copy number >10 in known genes that also overlaps a CpG island. Custom Tracks: Table browser searches

36. Intersecting custom tracks with available data (or other custom tracks) can be a powerful discovery tool.

37. Custom Tracks Table Browser Searches User-generated Data Externally Generated Data

38. Custom Tracks: User-generated Data

40. Custom Tracks Table Browser Searches User-generated Data Externally Generated Data

41. Custom Tracks from Outside Sources Custom tracks list shared by the community

42. Hands-on Session Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser Hands-on session for Basic Searches Gene Sorting search using the Gene Sorter Advanced searching using the Table Browser Custom Tracks Hands-on session for Sorter, Table Browser, and Custom Tracks