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

2. 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

3. A sample of what we will find:

4. Agenda 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

5. The UCSC Home page: genome.ucsc.edu navigate General information Specific information— new features, current status, etc.

6. The Genome Browser Gateway start page, basic search text/ID searches Helpful search examples, suggestions below Use this Gateway to search by: Gene names, symbols Chromosome number: chr7, or region: chr11:1038475-1075482 Keywords: kinase, receptor IDs: NP, NM, OMIM, and more… See lower part of page for help with format

7. The Genome Browser Gateway start page choices, February 2005 Make your Gateway choices: 1. Select Clade 2. Select 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 2 4 3 5 6

8. The Genome Browser Gateway sample search for Human BRCA1 Sample search: human, May 2004 assembly, BRCA1 Often you will have to select the right gene from a results list Sometimes, you will go directly to a browser image (use an ID) AF005068, breast cancer 1, early onset select

9. Overview of the whole Genome Browser page (first day, new human release) } Genome viewer section Track and image controls (day 1 = 40 tracks)

10. Overview of the whole Genome Browser page (mature release) } Genome viewer section mRNA and EST Tracks Expression and Regulation Comparative Genomics ENCODE Tracks Variation and Repeats Groups of data Mapping and Sequencing Tracks Genes and Gene Prediction Tracks

11. Different species, different tracks, same software

12. Sample Genome Viewer image, BRCA1 region Genome backbone STS markers Known genes RefSeq genes Gene predictions GenBank mRNAs repeats GenBank ESTs conservation SNPs CCDS

13. Visual Cues on the Genome Browser Track colors may have meaning—for example, Known Gene track: If there is a corresponding PDB entry, = black If there is a corresponding NCBI Reviewed seq, = dark blue If there is a corresponding NCBI Provisional seq, = light blue Tick marks; a single location (STS, SNP) Intron, and direction of transcription >> < exon < < << < ex 5' UTR3' UTR For some tracks, the height of a bar is increased likelihood of an evolutionary relationship

14. Options for changing the images: upper section Change your view 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

15. Annotation Track display options Some data is ON or OFF by default Links to details and/or filters Menu links to info about the tracks: content, methods Change track view You change the view with pulldown menus enforce changes After making changes, REFRESH to enforce the change

16. 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

17. Reset, Hide, Configure or Refresh to change settings You control the view Use pulldown menus Configure options page reset, back to defaults to start from scratch enforce the changes (hide, full, squish…)

18. Annotation Track options, if altered…. important point: the browser remembers! Session information (the position you were examining) Track choices (squish, pack, full, etc) Filter parameters (if you changed the colors of any items, or the subset to be displayed) …are all saved on your computer. When you come back in a couple of days to use it again, these will still be set. You may— or may not—intend this. To clear your “cart” or parameters, click default tracks OR

19. Clicking an annotation line, new page of detailed information You will get detail for that single item you click Example: click on the BRCA1 Black “Known Genes” line Click the line New web page opens Many details and links to more data about BRCA1

20. Click annotation track = BRCA1 “Known gene” detail page informative description other resource links microarray data mRNA secondary structure links to sequences protein domains/structure homologs in other species Gene Ontology™ descriptions mRNA descriptions pathways Not all genes have This much detail. Different annotation tracks carry different detail data. SNP detail page sample

21. Getting the sequences Get DNA, with Extended Options; or Details pages Use the DNA link at the top Plain or Extended options Change colors, fonts, etc.

22. Genomic (many options) mRNA Protein Getting the sequences Another way: from details pages Click a track, go to Sequence section of details page Click the line

23. Agenda 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

24. Accessing the BLAT tool Rapid searches by INDEXING the entire genome Works best with high similarity matches See documentation and publication for details BLAT = BLAST-like Alignment Tool

25. BLAT tool overview: www.openhelix.com/sampleseqs.html Submit Make choices DNA limit 25000 bases Protein limit 10000 aa 25 total sequences Paste one or more sequences Or upload

26. BLAT results, with links Results with demo sequences, settings default; sort = Query, Score Score is a count of matches—higher number, better match sorting Click browser to go to Genome Browser image location (next slide) Click details to see the alignment to genomic sequence (2 nd slide)

27. BLAT results, alignment details browser From browser click in BLAT results A new line with your Sequence from BLAT Search appears! query matches Click to flip frame Watch out for reading frame! Click - - - > to flip frame Base position = full and zoomed in enough to see amino acids

28. BLAT results, alignment details Your query Genomic match, color cues Side-by-side alignment

29. Agenda 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. 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)

31. 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

32. Proteome Browser Access from homepage or Known Gene pages Exon diagram, amino acids Many protein properties (pI, mw, composition, 3D…) more protein data

33. Agenda 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

34. 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

35. UCSC Genome Browser credits Led by David Haussler and Jim Kent Dozens of staff and students also work to 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

36. Agenda Basic searches using the Genome Browser Text searching, Sequence Searching (BLAT) In Silico PCR, Proteome Browser