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3. Version14c_0908 Copyright OpenHelix. No use or reproduction without express written consent 3 The UCSC Genome Browser Additional Tools Materials prepared by Warren C. Lathe III, Ph.D. Mary Mangan, Ph.D. www.openhelix.com Updated: Q3 2008

4. Copyright OpenHelix. No use or reproduction without express written consent4 UCSC Genome Browser Agenda UCSC Genome Browser: http://genome.ucsc.edu Introduction Gene Sorter in silico PCR VisiGene Browser Proteome Browser Other Features Exercises Introduction

5. Copyright OpenHelix. No use or reproduction without express written consent5 The UCSC Homepage: http://genome.ucsc.edu

6. Copyright OpenHelix. No use or reproduction without express written consent6 UCSC Genome Browser Agenda UCSC Genome Browser: http://genome.ucsc.edu Introduction Gene Sorter in silico PCR VisiGene Browser Proteome Browser Other Features Exercises

7. Copyright OpenHelix. No use or reproduction without express written consent77 Gene Sorter From homepage select “Gene Sorter”

8. Copyright OpenHelix. No use or reproduction without xpress written consent88 Gene Sorter Example Sort genes by similarity criteria

9. Copyright OpenHelix. No use or reproduction without express written consent99 Choose Genome Choose Assembly Type in gene name or accession number Gene Sorter: Chose Genome and Gene

10. Copyright OpenHelix. No use or reproduction without express written consent10 Gene Sorter: Similarity Sorting Options Choose from several similarity sorting options, varies by assembly & species

11. Copyright OpenHelix. No use or reproduction without express written consent11 Gene Sorter: Configure Configure Choose columns of data to display Choose order of display columns Some columns can be configured

12. Copyright OpenHelix. No use or reproduction without express written consent12 Gene Sorter: Saving Configuration Configure Hide, show all columns or return to default Save configurations and load previous

13. Copyright OpenHelix. No use or reproduction without express written consent13 Gene Sorter: Adding Custom Data Configure Custom columns of user’s data Custom data

14. Copyright OpenHelix. No use or reproduction without express written consent14 Gene Sorter: Filters Filter Filter data of columns displayed or those not displayed List genes List all genes found with selected filters

15. Copyright OpenHelix. No use or reproduction without express written consent15 Gene Sorter: Save Filters Save filter trim_name Click save

16. Copyright OpenHelix. No use or reproduction without express written consent16 Gene Sorter: Load Filters Saved filtersChoose filter & load

17. Copyright OpenHelix. No use or reproduction without express written consent17 Gene Sorter: Submit Filters Submit

18. Copyright OpenHelix. No use or reproduction without express written consent18 Gene Sorter: Get Results Go to results

19. Copyright OpenHelix. No use or reproduction without express written consent19 Gene Sorter: Sort Results by Name Re-sort Re-sort genes based on gene clicked using same parameters. Description

20. Copyright OpenHelix. No use or reproduction without express written consent20 Gene Sorter: VisiGene Results VisiGene Open UCSC VisiGene image page for gene.

21. Copyright OpenHelix. No use or reproduction without express written consent21 Gene Sorter: Alignment Results Alignment Amino acid alignment between reference gene and gene protein products

22. Copyright OpenHelix. No use or reproduction without express written consent22 Gene Sorter: Open Genome Browser Browser Open Genome Browser to location of chosen gene

23. Copyright OpenHelix. No use or reproduction without express written consent23 Gene Sorter: Open Details Page Description Open gene details page of chosen gene

24. Copyright OpenHelix. No use or reproduction without express written consent24 Gene Sorter: Gene Sequences Sequences Get sequences Choose sequence type, obtain FASTA file of all gene sequences

25. Copyright OpenHelix. No use or reproduction without express written consent25 Gene Sorter: Text File of Data Data text Obtain tab-delineated file of all displayed gene data

26. Copyright OpenHelix. No use or reproduction without express written consent26 Gene Sorter Sort genes by similarity criteria

27. Copyright OpenHelix. No use or reproduction without express written consent27 UCSC Genome Browser Agenda UCSC Genome Browser: http://genome.ucsc.edu Introduction Gene Sorter in silico PCR VisiGene Browser Proteome Browser Other Features Exercises

28. Copyright OpenHelix. No use or reproduction without express written consent28 In-Silico PCR: Find Genomic Sequence using Primers Select genome Enter primers Minimum 15 bases Flip reverse primer? Submit (note: the tool does not handle ambiguous bases at this time—don’t use Ns)

29. Copyright OpenHelix. No use or reproduction without express written consent29 In-Silico PCR Results Genomic location shown, links to Genome Viewer locationyour primers Your primers displayed, flipped if necessary Predicted genomic sequence shown Tm for primers Primer melting temperatures provided size Product size shown

30. Copyright OpenHelix. No use or reproduction without express written consent30 UCSC Genome Browser Agenda UCSC Genome Browser: http://genome.ucsc.edu Introduction Gene Sorter in silico PCR VisiGene Browser Proteome Browser Other Features Exercises

31. Copyright OpenHelix. No use or reproduction without express written consent31 VisiGene Image Browser VisiGene: Biological image data Expression in cells and tissues; mRNA or protein Search by symbol, author, body parts, IDs, stages…

32. Copyright OpenHelix. No use or reproduction without express written consent32 VisiGene Results List of results Select one to view Links and details

33. Copyright OpenHelix. No use or reproduction without express written consent33 UCSC Genome Browser Agenda UCSC Genome Browser: http://genome.ucsc.edu Introduction Gene Sorter in silico PCR VisiGene Browser Proteome Browser Other Features Exercises

34. Copyright OpenHelix. No use or reproduction without express written consent34 Proteome Browser Collection of protein level data Access from homepage or UCSC Gene pages

35. Copyright OpenHelix. No use or reproduction without express written consent35 Proteome Browser Results Protein level data Exons illustrated, link to browser Domains, family Structure Pathways

36. Copyright OpenHelix. No use or reproduction without express written consent36 UCSC Genome Browser Agenda UCSC Genome Browser: http://genome.ucsc.edu Introduction Gene Sorter in silico PCR VisiGene Browser Proteome Browser Other Features Exercises

37. Copyright OpenHelix. No use or reproduction without express written consent37 Other Features Utilities: other small useful tools liftOver: to migrate between genome versions Dusters: to clean up stray characters in sequence files Tree Maker

38. Copyright OpenHelix. No use or reproduction without express written consent38 Explore! genomewiki.ucsc.edu

39. Copyright OpenHelix. No use or reproduction without express written consent39 UCSC Genome Browser Agenda UCSC Genome Browser: http://genome.ucsc.edu Introduction Gene Sorter in silico PCR VisiGene Browser Proteome Browser Other Features Exercises

40. Copyright OpenHelix. No use or reproduction without express written consent40 Hands-on session for UCSC Additional Tools Exercises on the handouts We will walk through them together 2 styles: questions only, and step-by-step When we are finished the formal exercises, we can help you to investigate issues that you want to understand for your research

41. Copyright OpenHelix. No use or reproduction without express written consent41 Notice: The materials and slides offered are for non-commercial use only. Reproduction, distribution and/or use for commercial purposes is strictly prohibited. Copyright 2008, OpenHelix, LLC http://www.openhelix.com/ucsc