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

2. Copyright OpenHelix. No use or reproduction without express written consent2 A sample of what we will find:

3. Copyright OpenHelix. No use or reproduction without express written consent3 The UCSC Home page: genome.ucsc.edu navigate General information Specific information— new features, current status, etc.

4. Copyright OpenHelix. No use or reproduction without express written consent4 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

5. Copyright OpenHelix. No use or reproduction without express written consent5 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

6. Copyright OpenHelix. No use or reproduction without express written consent6 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

7. Copyright OpenHelix. No use or reproduction without express written consent7 Overview of the whole Genome Browser page (first day, new human release) } Genome viewer section Track and image controls (day 1 = 40 tracks)

8. Copyright OpenHelix. No use or reproduction without express written consent8 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

9. Copyright OpenHelix. No use or reproduction without express written consent9 Different species, different tracks, same software

10. Copyright OpenHelix. No use or reproduction without express written consent10 Sample Genome Viewer image, BRCA1 region Genome backbone STS markers Known genes RefSeq genes Gene predictions GenBank mRNAs repeats GenBank ESTs conservation SNPs MGC clones

11. Copyright OpenHelix. No use or reproduction without express written consent11 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

12. Copyright OpenHelix. No use or reproduction without express written consent12 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

13. Copyright OpenHelix. No use or reproduction without express written consent13 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

14. Copyright OpenHelix. No use or reproduction without express written consent14 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.

15. Copyright OpenHelix. No use or reproduction without express written consent15 Accessing the BLAT tool Rapid searches by INDEXING the entire genome Works best with high similarity matches BLAT = BLAST-like Alignment Tool

16. Copyright OpenHelix. No use or reproduction without express written consent16 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

17. Copyright OpenHelix. No use or reproduction without express written consent17 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)

18. Copyright OpenHelix. No use or reproduction without express written consent18 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

19. Copyright OpenHelix. No use or reproduction without express written consent19 BLAT results, alignment details Your query Genomic match, color cues Side-by-side alignment

20. Copyright OpenHelix. No use or reproduction without express written consent20 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)

21. Copyright OpenHelix. No use or reproduction without express written consent21 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

22. Copyright OpenHelix. No use or reproduction without express written consent22 Proteome Browser Access from homepage or Known Gene pages Exon diagram, amino acids Many protein properties (pI, mw, composition, 3D…) more protein data

23. Copyright OpenHelix. No use or reproduction without express written consent23 Gene Sorter From homepage select ‘Gene sorter’

24. Copyright OpenHelix. No use or reproduction without express written consent24 Gene Sorter interface Sorts genes by several criteria

25. Copyright OpenHelix. No use or reproduction without express written consent25 Gene Sorter interface Choose from 11 sorting options

26. Copyright OpenHelix. No use or reproduction without express written consent26 Gene Sorter results