1. Browsing the Genome Using Genome Browsers to Visualize and Mine Data

2. Genome Browsers Software designed to enable a user to access and display sequence data Software designed to enable a user to access and display sequence data Provide a visual correlation for different types of information Provide a visual correlation for different types of information Organize large amounts of genome sequence data Organize large amounts of genome sequence data

3. Several Different Genome Browsers Common features: Common features: Coordinate system is based on the build Coordinate system is based on the build Zoom in and out Zoom in and out Gene features aligned to genome Gene features aligned to genome Major Differences: Major Differences: Each Browser has a very different look and feel Each Browser has a very different look and feel Navigating through the information Navigating through the information

4. Main Genome Browser Repositories Ensembl Ensembl NCBI (Entrez) - BLAST NCBI (Entrez) - BLAST UCSC - BLAT UCSC - BLAT Ensembl, NCBI, and UCSC use the same human genome assembly that is generated by NCBI but release timing is different between sites Ensembl, NCBI, and UCSC use the same human genome assembly that is generated by NCBI but release timing is different between sites

5. UCSC Vertebrates, Deuterostomes, Insects, Nematodes, Yeast Vertebrates, Deuterostomes, Insects, Nematodes, Yeast Entry into genome sequence via BLAT Entry into genome sequence via BLAT Table Browser Table Browser Creation of PDF Creation of PDF Provides access to all the data produced by the project, and to the software used to analyze and present it Provides access to all the data produced by the project, and to the software used to analyze and present it Site produces and maintains annotation tracks Site produces and maintains annotation tracks

6. Aligned Annotation Tracks Genomic data: known genes, predicted genes, ESTs, mRNAs, CpG islands, assembly gaps and coverage, chromosomal bands, mouse homologies, and more Genomic data: known genes, predicted genes, ESTs, mRNAs, CpG islands, assembly gaps and coverage, chromosomal bands, mouse homologies, and more Annotation tracks are both computed at UCSC from publicly available sequence data and provided by collaborators Annotation tracks are both computed at UCSC from publicly available sequence data and provided by collaborators Users can also add their own custom tracks to the browser Users can also add their own custom tracks to the browser

7. UCSC Outline Navigating Navigating Configuring Browser Configuring Browser Extracting data Extracting data

8. Home Page

9. BLAT

10. BLAT Results

11. Standard Query

12. Query Results

13. Graphical Interface

14. Configuring Display

15. Components

16. Get DNA

17. Configuring DNA

18. DNA STS Highlighted

19. Tracks

20. Track Display

21. Human SDAD1

22. Convert

23. Mouse Sdad1

24. EST Track

25. Entry Data

26. Viewing Exons

27. Integrate Specific Data

28. Custom Tracks User provided annotation data User provided annotation data Can be in standard GFF format or in a format designed specifically for UCSC Genome Browser, including GTF, PSL, BED, WIG, and microarray (BED15) Can be in standard GFF format or in a format designed specifically for UCSC Genome Browser, including GTF, PSL, BED, WIG, and microarray (BED15)

29. Add Custom Tracks

30. Sample Custom Tracks GFF GFF chr5 EST exon 92719127 92719406. + 0 BE chr5 EST exon 92731587 92731784. + 0 BE Bed Bed chr5 92715320 92715326 miR-194 1 - chr5 92715467 92715474 miR-124.1 3 - chr5 92715467 92715473 miR-124/506 1 -

31. Display of Custom Tracks

32. Configure Track Display

33. Save PDF

34. Table Browser

35. Sample Table Data

36. Proteome Browser

37. Protein Sequence

38. Protein Characteristics

39. Structure Information

40. Summary of UCSC Different ways of querying genome Different ways of querying genome Control over graphical display Control over graphical display Vast amount of genomic data Vast amount of genomic data Ability to collect that data Ability to collect that data

41. However UCSC does not include my genome UCSC does not include my genome Actually no genome browser supports my genome Actually no genome browser supports my genome

42. Custom Browser Software GBrowse is a combination of database and interactive Web page for manipulating and displaying annotations on genomes GBrowse is a combination of database and interactive Web page for manipulating and displaying annotations on genomes Annotation Browsers- Argo and Apollo Annotation Browsers- Argo and Apollo