1. Copyright OpenHelix. No use or reproduction without express written consent1

2. 2 Important note to slide users: To maintain the color schemes/cues and the animations, if you import these slides into other slide sets please click the checkbox in the PowerPoint Insert window that maintains slide format. Otherwise important information may be lost. Mac usersPC users

3. Version13a_0708 Copyright OpenHelix. No use or reproduction without express written consent 3 The UCSC Genome Browser Introduction Materials prepared by Mary Mangan, Ph.D. www.openhelix.com Updated: Q3 2008

4. Copyright OpenHelix. No use or reproduction without express written consent4 Organization of Genomic Data Genome backbone: base position number sequence Annotation Tracks chromosome band known genes predicted genes evolutionary conservation SNPs sts sites gap locations repeated regions microarray/expression data more… Links out to more data

5. Copyright OpenHelix. No use or reproduction without express written consent5 A Sample of the UCSC Genome Browser gene details Annotation Tracks official sequence comparisons SNPs

6. Copyright OpenHelix. No use or reproduction without express written consent6 UCSC Genome Browser Credits Led by David Haussler and Jim Kent Dozens of staff and students bring you this software and data Development team: http://genome.ucsc.edu/staff.html http://genome.ucsc.edu/goldenPath/credits.html Funding, data sources, external contributors

7. Copyright OpenHelix. No use or reproduction without express written consent7 UCSC Genome Browser Agenda UCSC Genome Browser: http://genome.ucsc.edu Introduction and Credits Basic Searches Understanding Displays Get Details or Sequences Sequence Searches (BLAT) in silico PCR Proteome Browser VisiGene Browser Exercises

8. Copyright OpenHelix. No use or reproduction without express written consent8 The UCSC Homepage: http://genome.ucsc.edu navigate General information Specific information— new features, current status, etc.

9. Copyright OpenHelix. No use or reproduction without express written consent9 Genome Browser Gateway: start page, basic search text/ID searches Helpful search examples, suggestions below Use this Gateway to search by: Gene names, symbols, IDs Chromosome number: chr7, or region: chr11:1038475-1075482 Keywords: kinase, receptor See lower part of page for help with format

10. Copyright OpenHelix. No use or reproduction without express written consent10 The Genome Browser Gateway Make your Gateway choices: 1. Select Clade 2. Select genome = species: search 1 species at a time 3. Assembly: the official backbone DNA sequence 4. Position: location in the genome to examine 5. Image width: how many pixels in display window; 5000 max 6. Configure: make fonts bigger + other choices 1 45 6 3 2

11. Copyright OpenHelix. No use or reproduction without express written consent11 The Genome Browser Gateway sample search for Human TP53 Sample search: human, March 2006 assembly, tp53 select Select from results list ID search may go right to a viewer page, if unique

12. Copyright OpenHelix. No use or reproduction without express written consent12 Overview of the Whole Genome Browser Page (mature release) } Genome viewer section mRNA and EST Tracks Expression and Regulation Comparative Genomics As a group Individual species Variation and Repeats Groups of data (Tracks) Mapping and Sequencing Tracks Genes and Gene Prediction Tracks ENCODE Tracks Phenotype and Disease Tracks

13. Copyright OpenHelix. No use or reproduction without express written consent13 Different Species, Different Tracks, Same Software Species may have different data tracks Layout, software, functions the same

14. Copyright OpenHelix. No use or reproduction without express written consent14 Sample Genome Viewer Image, TP53 Region base position UCSC genes RefSeq genes mRNAs & ESTs repeats 28 species compared SNPs single species compared MGC clones

15. Copyright OpenHelix. No use or reproduction without express written consent15 Visual Cues on the Genome Browser Track colors may have meaning—for example, UCSC Gene track: If there is a corresponding PDB entry, = black If there is a corresponding reviewed/validated seq, = dark blue If there is a non-RefSeq seq, = lightest blue Tick marks; a single location (STS, SNP) For some tracks, the height of a bar is increased likelihood of an evolutionary relationship (conservation track) Intron, and direction of transcription >> < exon < < << < ex 5' UTR3' UTR

16. Copyright OpenHelix. No use or reproduction without express written consent16 Options for Changing Images: Upper Section Change your view or location with controls at the top Use “base” to get right down to the nucleotides Configure: to change font, window size, more… Specify a position fonts, window, more Walk left or right Zoom in Zoom out click to zoom 3x and re-center

17. Copyright OpenHelix. No use or reproduction without express written consent17 Annotation Track Display Options Some data is ON or OFF by default Links to info and/or filters Menu links to info about the tracks: content, methods You change the view with pulldown menus After making changes, REFRESH to enforce the change enforce changes enforce changes Change track view

18. Copyright OpenHelix. No use or reproduction without express written consent18 Annotation Track options, defined Hide: removes a track from view Dense: all items collapsed into a single line Squish: each item = separate line, but 50% height + packed Pack: each item separate, but efficiently stacked (full height) Full: each item on separate line

19. Copyright OpenHelix. No use or reproduction without express written consent19 Reset, Hide, Configure or Refresh to Change Settings You control the views Use pulldown menus Configure options page reset, back to defaults start from scratch enforce any changes (hide, full, squish…) Flip display to Genomic 3’  5’

20. Copyright OpenHelix. No use or reproduction without express written consent20 Cookies and Sessions Your browser remembers where you were (cookies) To clear your “cart” or parameters, click default tracks or reset OR Save your setup as “sessions” and store/share them

21. Copyright OpenHelix. No use or reproduction without express written consent21 Click Any Viewer Object for Details Example: click your mouse anywhere on the TP53 line Click the item New description web page opens Many details and links to more data about TP53

22. Copyright OpenHelix. No use or reproduction without express written consent22 Click Annotation Track Item for Details Pages Not all genes have this much detail. Different annotation tracks carry different data. informative description other resource links microarray data mRNA secondary structure links to sequences protein domains/structure orthologs in other species Gene Ontology™ descriptions mRNA descriptions pathways genetic association studies comparative toxicology gene model

23. Copyright OpenHelix. No use or reproduction without express written consent23 Get DNA, with Extended Case/Color Options Use the DNA link at the top Plain or Extended options Change colors, fonts, etc.

24. Copyright OpenHelix. No use or reproduction without express written consent24 Get Sequence from Details Pages Click a track, go to Sequence section of details page Click the item sequence section on detail page

25. Copyright OpenHelix. No use or reproduction without express written consent25 UCSC Genome Browser Agenda UCSC Genome Browser: http://genome.ucsc.edu Introduction and Credits Basic Searches Understanding Displays Get Details or Sequences Sequence Searches (BLAT) in silico PCR Proteome Browser VisiGene Browser Exercises

26. Copyright OpenHelix. No use or reproduction without express written consent26 Accessing the BLAT Tool Rapid searches by INDEXING the entire genome Works best with high similarity matches See documentation and publication for details Kent, WJ. Genome Res. 2002. 12:656 BLAT = BLAST-like Alignment Tool

27. Copyright OpenHelix. No use or reproduction without express written consent27 BLAT Tool Overview: www.openhelix.com/sampleseqs.html Make choices DNA limit 25000 bases Protein limit 10000 aa 25 total sequences Paste one or more sequences Or upload submit

28. Copyright OpenHelix. No use or reproduction without express written consent28 BLAT Results with Hyperlinks Results with demo sequences, settings default; sort = Query, Score Score is a count of matches—higher number, better match Click browser to go to Genome Browser image location (next slide) Click details to see the alignment to genomic sequence (2 nd slide) sorting go to browser/viewergo to alignment detail

29. Copyright OpenHelix. No use or reproduction without express written consent29 BLAT Results: Browser From browser click in BLAT results A new line with Your Sequence from BLAT Search appears! Base position = “full” menu and zoomed in enough to see amino acids in 3 frame translation query

30. Copyright OpenHelix. No use or reproduction without express written consent30 BLAT Results, Alignment Details Your query Genomic match, color cues Side-by-side alignment yours genomic

31. Copyright OpenHelix. No use or reproduction without express written consent31 UCSC Genome Browser Agenda UCSC Genome Browser: http://genome.ucsc.edu Introduction and Credits Basic Searches Understanding Displays Get Details or Sequences Sequence Searches (BLAT) in silico PCR Proteome Browser VisiGene Browser Exercises

32. Copyright OpenHelix. No use or reproduction without express written consent32 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)

33. Copyright OpenHelix. No use or reproduction without express written consent33 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

34. Copyright OpenHelix. No use or reproduction without express written consent34 Proteome Browser Access from homepage or UCSC Gene pages Exon diagram, amino acids… Many protein properties (pI, mw, composition, 3D…) more data

35. Copyright OpenHelix. No use or reproduction without express written consent35 VisiGene Image Browser VisiGene: Biological image data Expression in cells and tissues; mRNA or protein Search by symbol, author, body parts, IDs, stages…

36. Copyright OpenHelix. No use or reproduction without express written consent36 UCSC Genome Browser Agenda UCSC Genome Browser: http://genome.ucsc.edu Introduction and Credits Basic Searches Understanding Displays Get Details or Sequences Sequence Searches (BLAT) in silico PCR Proteome Browser VisiGene Browser Exercises

37. Copyright OpenHelix. No use or reproduction without express written consent37 Hands-on session for basic searches 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

38. Copyright OpenHelix. No use or reproduction without express written consent38 Notice: The materials and slides offered are for non-commercial use only. Reproduction, distribution and/or use for commercial purposes is strictly prohibited. Copyright 2006, OpenHelix, LLC http://www.openhelix.com/ucscmaterials.shtml

39. Copyright OpenHelix. No use or reproduction without express written consent39 Overview of the whole Genome Browser page (first day, new human release) Tracks are added to an assembly over time Not all are present in a new release at first } Genome viewer section Track and image controls (day 1 = 40 tracks)