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

2. VISTA Materials prepared by: Warren C. Lathe III Mary E. Mangan www.openhelix.com Version_3

3. Copyright OpenHelix. No use or reproduction without express written consent3 VISTA Agenda Introduction and Credits VISTA Servers mVISTA rVISTA GenomeVISTA wgVISTA VISTA Precomputed Alignments VISTA Browser VISTA-Point Whole Genome rVISTA Summary Exercises VISTA resource: http://genome.lbl.gov/vista Introduction and Credits

4. Copyright OpenHelix. No use or reproduction without express written consent4 Comparative Genomics Introduction Human Drosophila Mouse Urchin Chimp Similar Genes Synteny Sequence Alignment

5. Copyright OpenHelix. No use or reproduction without express written consent5 Comparative Genomics Introduction  VISTA: focus is comparative genomics  Broad range of species for comparative analysis (animals, plants, fungi, bacteria)  Full set of pre-computed comparative data  Comparative analysis of user-submitted data

6. Copyright OpenHelix. No use or reproduction without express written consent6 VISTA Homepage VISTA Servers (submit your own data) VISTA Browsers (precomputed alignments) Other VISTA-related Projects VISTA homepage: http://genome.lbl.gov/vista Access servers, browsers, other information

7. Copyright OpenHelix. No use or reproduction without express written consent7 VISTA Introduction “sliding window” to measure sequence conservation (default window size 100bp) Graphical presentation of sequence conservation as “peaks-and-valley” curve >70% identity base sequence coordinates % identity

8. Copyright OpenHelix. No use or reproduction without express written consent8 wgVISTA Align and compare sequences, including microbial assemblies mVISTA Align and compare sequences rVISTA Search for TFBS combined with a comparative sequence analysis VISTA Servers GenomeVISTA Align DNA sequence to a genome

9. Copyright OpenHelix. No use or reproduction without express written consent9 VISTA Browser Browse through pre-computed whole-genome alignments Whole Genome rVISTA Whole genome analysis for conserved TFBS over-represented in upstream regions of genes Precomputed Alignments VISTA-Point Browse and obtain sequence and alignment data

10. Copyright OpenHelix. No use or reproduction without express written consent 10 SNP-VISTA Visualization of mutations in genes and discovery of recombination points VISTA Overview: Other Projects TreeQ-VISTA Interactive tree visualization tool Enhancer Browser Exploration of human enhancer activity Phylo-VISTA Using phylogenetic relationships to visualize DNA similarity

11. Copyright OpenHelix. No use or reproduction without express written consent11 VISTA Credits Developed & hosted at the Genomics Division of Lawrence Berkeley National Laboratory Collaboration & Contribution UC Berkeley Stanford UC Davis Supported by the Office of Biological and Environmental Research, US DOE.

12. Copyright OpenHelix. No use or reproduction without express written consent12 Publications Publications and citation information Access to downloads

13. Copyright OpenHelix. No use or reproduction without express written consent13 VISTA Agenda VISTA resource: http://genome.lbl.gov/vista Introduction and Credits VISTA Servers mVISTA rVISTA GenomeVISTA wgVISTA VISTA Precomputed Alignments VISTA Browser VISTA-Point Whole Genome rVISTA Summary Exercises

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

15. Copyright OpenHelix. No use or reproduction without express written consent15 mVISTA: Interface Our example will show 3 sequences Align up to 100 sequences

16. Copyright OpenHelix. No use or reproduction without express written consent16 mVISTA: Input of Sequences Provide your email address Upload your sequences Or enter GenBank ID your email upload file or GenBank ID

17. Copyright OpenHelix. No use or reproduction without express written consent17 AVID multiple pair wise alignments accepts finished or draft sequences LAGAN true multiple alignments mVISTA: Input Parameters Shuffle-LAGAN multiple pair wise alignments detects sequence rearrangements and inversions

18. Copyright OpenHelix. No use or reproduction without express written consent18 mVISTA: Input Parameters

19. Copyright OpenHelix. No use or reproduction without express written consent19 mVISTA: Results PDF VISTA Browser VISTA-Point

20. Copyright OpenHelix. No use or reproduction without express written consent20 rVISTA: Access

21. Copyright OpenHelix. No use or reproduction without express written consent21 rVISTA: Interface your email sequences rVISTA sequence submission: set number Submit email address, sequences, and set parameters Key step: click the box for: Find potential transcription factors

22. Copyright OpenHelix. No use or reproduction without express written consent22 rVISTA: Select TRANSFAC Matrices

23. Copyright OpenHelix. No use or reproduction without express written consent23 rVISTA: Mailed Results Emailed results will provide a link Choose which binding sites matrices to display You can then choose visualization options display

24. Copyright OpenHelix. No use or reproduction without express written consent24 rVISTA: Results Graphic Blue all transcription factor (TF) binding sites Red TF sites which are aligned in both sequences Green TF sites which are aligned & in conserved regions sequences sites

25. Copyright OpenHelix. No use or reproduction without express written consent25 GenomeVISTA: Access

26. Copyright OpenHelix. No use or reproduction without express written consent26 GenomeVISTA: Input paste sequence or upload file or GenBank ID compare to

27. our query Copyright OpenHelix. No use or reproduction without express written consent27 GenomeVISTA: Results VISTA Track VISTA-Point VISTA Browser

28. Copyright OpenHelix. No use or reproduction without express written consent28 wgVISTA: Large Scale Sequence Comparison wgVISTA: whole genome VISTA Compares 2 sequences (up to 10 Mb) Draft or finished microbial assembly sequences can be used

29. Copyright OpenHelix. No use or reproduction without express written consent29 VISTA Agenda VISTA resource: http://genome.lbl.gov/vista Introduction and Credits VISTA Servers mVISTA rVISTA GenomeVISTA wgVISTA VISTA Precomputed Alignments VISTA Browser VISTA-Point Whole Genome rVISTA Summary Exercises

30. Copyright OpenHelix. No use or reproduction without express written consent30 VISTA Browser: Access

31. Copyright OpenHelix. No use or reproduction without express written consent31 VISTA Browser: Input Menu genomeposition visualization Java 2, if needed Choose “base” genome Select location Determine visualization preference VISTA Browser VISTA tracks on UCSC Browser VISTA-Point

32. Copyright OpenHelix. No use or reproduction without express written consent32 VISTA Browser: Base Genome Human May 2006 Select a genome Note: new versions and species added over time

33. Copyright OpenHelix. No use or reproduction without express written consent33 VISTA Browser: Position Can be coordinates: chr9:104622838-104769991 Can be a gene symbol or name If multiple matches, select from list select symbolname

34. Copyright OpenHelix. No use or reproduction without express written consent34 VISTA Browser: Result Position on chromosome Control Panel Graphical display of genome alignments Color Legend Cursor Info Menu & Icons Curve annotation (species) 1 row

35. Copyright OpenHelix. No use or reproduction without express written consent35 VISTA Browser: Alignment Details direction exon repeats alignment SNPs gene

36. Copyright OpenHelix. No use or reproduction without express written consent36 VISTA Browser: Options Print / SaveShift displayed region to left or rightEnlarge / Shrink alignment displayed region Add / Remove selected alignment Undo / Redo

37. Copyright OpenHelix. No use or reproduction without express written consent37 VISTA Browser: Options Access all alignment-related information and more Retrieve sequence alignment of displayed region Alter display parameterAccess UCSC Genome Browser with VISTA TracksGet help

38. Copyright OpenHelix. No use or reproduction without express written consent38 VISTA Browser: Control Panel change base change position change annotation add species add/remove rows see nucleotides

39. Copyright OpenHelix. No use or reproduction without express written consent39 VISTA Browser: Add Species select different dog genome alignment

40. Copyright OpenHelix. No use or reproduction without express written consent40 VISTA Browser: Curve Parameter Panel Default settings for new species curve See manual for parameter details Change later with “curve parameters” button

41. Copyright OpenHelix. No use or reproduction without express written consent41 VISTA Browser: Zooming vs. rhesus vs. dog

42. Copyright OpenHelix. No use or reproduction without express written consent42 VISTA Browser: Viewing Contigs contigs

43. Copyright OpenHelix. No use or reproduction without express written consent43 VISTA Browser: Alignment Details click here Click an alignment or annotation to select it Then “i” button for information

44. Copyright OpenHelix. No use or reproduction without express written consent44 VISTA Browser: Access to UCSC Browser

45. Copyright OpenHelix. No use or reproduction without express written consent45 VISTA Browser: rankVISTA Graphic

46. Copyright OpenHelix. No use or reproduction without express written consent46 VISTA Browser: rankVISTA Graphic rankVISTA data

47. click here VISTA Point: Introduction Copyright OpenHelix. No use or reproduction without express written consent47

48. VISTA Point: Access Overview Copyright OpenHelix. No use or reproduction without express written consent48

49. VISTA Point: Navigation Copyright OpenHelix. No use or reproduction without express written consent49

50. VISTA Point: Navigation Copyright OpenHelix. No use or reproduction without express written consent50

51. VISTA Point: Graphics Table Copyright OpenHelix. No use or reproduction without express written consent51

52. VISTA Point: AlignmentsTable Copyright OpenHelix. No use or reproduction without express written consent52 sequence

53. VISTA Point: Alignments Table Copyright OpenHelix. No use or reproduction without express written consent53 align MFA CNS rVISTA

54. Copyright OpenHelix. No use or reproduction without express written consent54 Whole Genome rVISTA: Access

55. Copyright OpenHelix. No use or reproduction without express written consent55 Whole Genome rVISTA: Select Alignment IDs or symbols upstream range

56. Copyright OpenHelix. No use or reproduction without express written consent56 Whole Genome rVISTA: Results sites found view genes

57. Copyright OpenHelix. No use or reproduction without express written consent57 Whole Genome rVISTA: Gene Results

58. Copyright OpenHelix. No use or reproduction without express written consent58 VISTA Agenda VISTA resource: http://genome.lbl.gov/vista Introduction and Credits VISTA Servers mVISTA rVISTA GenomeVISTA wgVISTA VISTA Precomputed Alignments VISTA Browser VISTA-Point Whole Genome rVISTA Summary Exercises

59. Copyright OpenHelix. No use or reproduction without express written consent59 VISTA Servers mVISTA: create your own sequence alignments rVISTA: identify conserved transcription factor binding sitesg sites GenomeVISTA: align your sequences with genomes wgVISTA:to align sequences up to 10 Mb

60. Copyright OpenHelix. No use or reproduction without express written consent60 VISTA Browser and rankVISTA Convenient tool to display genome alignments Display of multiple alignments to find conserved regions throughout various genomes Access to displayed alignment in various formats rhesus dog horse rankVISTA

61. VISTA Point Copyright OpenHelix. No use or reproduction without express written consent61

62. Copyright OpenHelix. No use or reproduction without express written consent62 VISTA-related Publications

63. Copyright OpenHelix. No use or reproduction without express written consent63 VISTA Summary VISTA Servers (submit your own data) Precomputed Alignments updates

64. Copyright OpenHelix. No use or reproduction without express written consent64 VISTA Agenda VISTA resource: http://genome.lbl.gov/vista Introduction and Credits VISTA Servers mVISTA rVISTA GenomeVISTA wgVISTA VISTA Precomputed Alignments VISTA Browser VISTA-Point Whole Genome rVISTA Summary Exercises