1. Tools in Bioinformatics Genome Browsers

2. Retrieving genomic information Previous lesson(s): annotation-based perspective of search/data Today: genomic-based perspective: look at all the data from the prism of a specific chromosome location Next: sequence-based searches

3. What should a good genome browser provide? Present all the available genomic info on a single plot Allow a highly customizable visualization Allowing researchers to add their own stuff Moving/Zooming freely Easily downloadable data

4. Genome browsers NCBI Map Viewer http://www.ncbi.nih.gov/mapview Ensembl http://www.ensembl.org/ UCSC Genome Browser http://genome.ucsc.edu/

5. UCSC Home page ( genome.ucsc.edu ) navigate General information Specific information— new features, current status, etc. UCSC Material developed by W.C. Lathe and M. Mangan, info@openhelix.com

6. The Genome Browser Gateway start page, basic search Start all text/ID searches here! Use this Gateway page to search by: gene names, gene symbols, chromosome number, region, keyword, identifiers (NP, NM, OMIM, LocusLink), and more. See examples on page for format Helpful search examples, suggestions below

7. The Genome Browser Gateway start page choices, sample search for Human BRCA1 Perform a sample search with the May 2004 data assembly, and examine the results. We will use human BRCA1 as our example. breast and ovarian cancer susceptibility gene, Science. 1994 Oct 7;266(5182):66-71 Use the Submit button to send the query to the database.

8. Results of our sample search 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) 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 Track and image controls (72 tracks = mature assembly) 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. First sample Genome Viewer image Genome backbone STS markers Known genes RefSeq genes Full-length clones if available Gene predictions GB human ESTs, mRNAs Microarray data if available species comparisons repeats

12. Different species, different tracks

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: Change your overview from the controls at the top Change viewer window size Use “base” to get right down to the nucleotides Specify a position How wide on screen Walk left or right Zoom in Zoom out

15. First sample Genome Viewer image Click on a line in the annotation tracks for more info…

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

17. “Known gene” BRCA1 sample page informative description other resource links microarray data mRNA secondary structure links to sequences protein domains and 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.

18. Getting the sequences 2 ways: get DNA or Extended options Use the DNA link at the top of the Viewer, simple or extended options Extended options to set colors, case, underline Choices here reflect displayed tracks

19. From the gene detail new page go to Sequence section: Getting the sequences From Gene Detail page Click a track, link down two levels to get that specific sequence Simple sequences, just this known gene Click the line

20. Annotation Track display options hide, dense, squish, pack, full…? Some data is ON or OFF by default Change track view You change the view with pulldown menus. refresh to make changes After changing a pulldown, REFRESH to commit the change Links to details and/or filters Menu links to info about tracks—content and methods.

21. Annotation Track options, defined Hide: removes a track from your image. Dense: all items collapsed into a single line. Squish: each item = separate line, but 50% height + packed Pack: each item separate, but efficiently stacked (but full height) Full: each item on a separate line.

22. 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 reset all OR

23. Other image display options back to defaults to start from scratch make the changes specified (hide, full, squish, dense…) You control the view, with pulldown menus and these other options. new!

24. Table browser: Output formats Fasta file of sequence data

25. SFRS5 examples

26. SFRS11 Example

27. SFRS7