1. Genomics and Personalized Care in Health Systems Lecture 5 Genome Browser Leming Zhou, PhD School of Health and Rehabilitation Sciences Department of Health Information Management

2. Genome Browser Genome Browser is a computer program which helps to display gene maps, browse the chromosomes, align genes or gene models with ESTs or contigs etc. Big Three: –UCSC Genome Browser –NCBI Mapviewer –Ensemble

3. UCSC Genome Browser: http://genome.ucsc.edu

4. NCBI Mapviewer

5. Ensemble

6. The UCSC Genome Browser Slides adopted from OpenHelix training materials

7. UCSC Genome Browser http://genome.ucsc.edu

8. Genome Browser Gateway 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

9. Genome Browser Gateway

10. 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 45 1 3 2 assembly 6

11. The Genome Browser Gateway Sample search: human, March 2006 assembly, tp53 select Select from results list ID search may go right to a viewer page, if unique

12. Sample Genome Viewer Image, TP53 Region base position UCSC genes RefSeq genes mRNAs & ESTs repeats many species compared SNPs single species compared MGC clones

13. 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 Alignment indications (Conservation pairs: “chain” or “net” style) Alignments = boxes, Gaps = lines

14. 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… –Next item, next exon navigation assistance can be turned on Specify a position Fonts, window, next item, 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 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 change s Enforce changes Change track view Links to info and/or filters

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 Pack: each item separate, but efficiently stacked (full height) Full: each item on separate line

17. Mid-page Options 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’

18. 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

19. 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

20. Get DNA, with Extended Case/Color Options Use the DNA link at the top Plain or Extended options Change colors, fonts, etc.

21. Base Level and Protein Sequences

22. BLASTX Search to Confirm the Protein

23. Get Sequence from Details Pages Click a track, go to Sequence section of details page Click the item sequence section on detail page

24. Accessing the BLAT Tool BLAT = BLAST-like Alignment Tool – Rapid searches by INDEXING the entire genome – Works best with high similarity matches

25. BLAT BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 25 bases, and sometimes find them down to 20 bases. BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more. In practice DNA BLAT works well on primates, and protein BLAT on land vertebrates BLAT works by keeping an index of the entire genome in memory. The index consists of all non-overlapping 11-mers except for those heavily involved in repeats. http://genome.ucsc.edu

26. BLAT Search Make choices DNA limit 25000 bases Protein limit 10000 aa 25 total sequences Paste one or more sequences Or upload submit

27. 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

28. 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

29. BLAT Results, Alignment Details Your query Genomic match, color cues Side by Side Alignment yours genomic

30. Summary UCSC Genome Browser Visual cues and genomic context Many ways to alter your views Access to deeper data Access and use sequence data

31. UCSC Table Browser

32. The Table Browser Open browser

33. Table Browser

34. 34 Many Other Databases Use UCSC Genome Browser Mirror and Software Malaria: http://areslab.ucsc.edu / Arabidopsis: http://epigenomics.mcdb.ucla.edu/ Archaea: http://archaea.ucsc.edu/ GSID HIV Browser: http://www.gsid.org/ GEP Drosophila Genome Browser : http://gander.wustl.edu http://gander.wustl.edu …

39. GEP Drosophila Genome Browser UCSC Genome Browser, GEP version, parts of genomes, GEP data, used for annotation of Drosophila species – http://gander.wustl.edu Male Drosophila melanogaster http://en.wikipedia.org/wiki/Drosophila_melanogaster

43. Drosophila melanogaster Chromosomes http://en.wikipedia.org/wiki/Drosophila_melanogaster

44. Fruit Flies and Human Disease Research About 75% of known human disease genes have a recognizable match in the genetic code of fruit flies, and 50% of fly protein sequences have mammalian analogues. An online database called Homophila is available to search for human disease gene homologues in flies and vice versa.Homophila Drosophila is being used as a genetic model for several human diseases including the neurodegenerative disorders Parkinson's, Huntington's, spinocerebellar ataxia and Alzheimer's disease. The fly is also being used to study mechanisms underlying aging and oxidative stress, immunity, diabetes, and cancer, as well as drug abuse.

45. Homework 4 Read through the BLAST tutorial (IntroToBLAST.zip, A simple Introduction to NCBI BLAST) and follow the instructions to reproduce the results described in the tutorial. List the steps you have taken and indicate whether you find any differences from the results mentioned in the tutorial. Use the sequence of BRCA1 gene, run a BLAT search against human genome (the most recent assembly, GRCh37), select the best sequence alignment result and view the output in the genome browser. You should provide a screen shot of the obtained page, which should include at least the gene, its homolog genes, other refseq, mRNA, the gene in other species, SNPs, and repeats. – Obtain mRNA-Genomic Alignments record from the browser – Obtain the predicted protein sequence from the browser – Obtain the precise location of one SNP record in the genome sequence – Zoom in to the base level and determine the protein sequence corresponding to one well conserved exon; get the DNA sequence of the exon, run a blastx search (do not apply low complexity filtering) to confirm the correctness of the protein sequence you obtain