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

2. VBRC: Viral Bioinformatics Resource Center Viral Data & Analysis Tools Materials prepared by: Cynthia Perreault-Micale, Ph.D. www.openhelix.com Updated: Q3 2009 Version 1.0_0609

3. Copyright OpenHelix. No use or reproduction without express written consent3 VBRC Agenda Introduction and Credits VBRC Resources Virus Orthologous Clusters (VOCs) VOCs Additional Features Additional Tools Summary Exercises VBRC: http://www.vbrc.orghttp://www.vbrc.org

4. VBRC Homepage Copyright OpenHelix. No use or reproduction without express written consent4 http://www.vbrc.org

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

6. News, Publications & More Homepage top navigation menu Copyright OpenHelix. No use or reproduction without express written consent6

7. A Variety of Analytical Tools & Resources Copyright OpenHelix. No use or reproduction without express written consent7 Contact http://www.vbrc.org

8. An Example Copyright OpenHelix. No use or reproduction without express written consent8 VBRC offers many resources & tools This shows genes common to 2 viral genomes From Graphical Ortholog Synteny Comparison tool A comprehensive database of viral information

9. Copyright OpenHelix. No use or reproduction without express written consent9 VBRC Agenda Introduction and Credits VBRC Resources Virus Orthologous Clusters (VOCs) VOCs Additional Features Additional Tools Summary Exercises VBRC: http://www.vbrc.orghttp://www.vbrc.org

10. To Access VBRC Resources: Copyright OpenHelix. No use or reproduction without express written consent10 Select data or analysis Click

11. Virus Descriptions Copyright OpenHelix. No use or reproduction without express written consent11 Click Help

12. Descriptions Copyright OpenHelix. No use or reproduction without express written consent12 Blog Posts General info & links Analysis tools Specific info & details

13. Available Genomes Copyright OpenHelix. No use or reproduction without express written consent13 Click here Or click here

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

15. Locating Strain-Specific Genome Information Copyright OpenHelix. No use or reproduction without express written consent15 Click

16. Strain-Specific Details, Links & Options Copyright OpenHelix. No use or reproduction without express written consent16 Click Options Download a genome in FASTA format or Zip archive Send to view in the Viral Genome Organizer browser

17. Homepage Data Tab – Sequence Section Copyright OpenHelix. No use or reproduction without express written consent17 Search for genes by name, position, weight, motif, PDB ID and more

18. Homepage Data Tab – Annotation Section Copyright OpenHelix. No use or reproduction without express written consent18

19. Analytical Tools Copyright OpenHelix. No use or reproduction without express written consent19 Or click here Click here

20. Similarity Searches Copyright OpenHelix. No use or reproduction without express written consent20 The major difference is how the alignment data are displayed Our focus is XS BLAST List format - scores at top, alignments below User-friendly format

21. XS BLAST Search Copyright OpenHelix. No use or reproduction without express written consent21 Click Enter email here Click

22. XS BLAST Search Options & Example Copyright OpenHelix. No use or reproduction without express written consent22 Input sequence Click Link to help - green icons

23. XS BLAST Search Results Copyright OpenHelix. No use or reproduction without express written consent23 Details of your search We will enlarge & examine the results table next

24. XS BLAST Search Results Table Copyright OpenHelix. No use or reproduction without express written consent24

25. XS BLAST Search Results Table – Part 2 Copyright OpenHelix. No use or reproduction without express written consent25

26. Accessing the Ortholog Comparison Tools Copyright OpenHelix. No use or reproduction without express written consent26 Click here

27. Ortholog Comparison Tools Copyright OpenHelix. No use or reproduction without express written consent27 Click 3 Ortholog Comparison tools are available Pairwise & Multi-genome Ortholog Comparison tools function similarly to display lists of genes shared or missing between genomes Graphical Ortholog Synteny data are graphical

28. Pairwise Ortholog Comparisons Copyright OpenHelix. No use or reproduction without express written consent28

29. Pairwise Ortholog Comparison Search Results Copyright OpenHelix. No use or reproduction without express written consent29

30. Click Graphical Ortholog Synteny Comparisons Copyright OpenHelix. No use or reproduction without express written consent30

31. Graphical Results Copyright OpenHelix. No use or reproduction without express written consent31 Genomes shown on x & y axes Dark & light blue marks show genes present on + or – strands, respectively Red & green marks show genes that align on opposing strands Black dots are for genes present in only one genome Key

32. Copyright OpenHelix. No use or reproduction without express written consent32 VBRC Agenda Introduction and Credits VBRC Resources Virus Orthologous Clusters (VOCs) VOCs Additional Features Additional Tools Summary Exercises VBRC: http://www.vbrc.orghttp://www.vbrc.org

33. Accessing Viral Orthologous Clusters (VOCs) Copyright OpenHelix. No use or reproduction without express written consent33 Click here Or click here Or here

34. VBRC Tools Copyright OpenHelix. No use or reproduction without express written consent34

35. VOCs Copyright OpenHelix. No use or reproduction without express written consent35 Click Help Java-based tool to search & extract genome, gene & protein data from VBRC Frequently updated, latest is PDB Scan

36. Viral Orthologous Clusters (VOCs) - Basics Copyright OpenHelix. No use or reproduction without express written consent36 Click First choose a database An empty VOCs search will open We will review filter tabs next Search options Filters

37. VOCs: Sequence Filter – Top Section Copyright OpenHelix. No use or reproduction without express written consent37

38. VOCs: Sequence Filter – Lower Section Copyright OpenHelix. No use or reproduction without express written consent38 Click

39. VOCs: Sequence Filter – DNA Constraints Copyright OpenHelix. No use or reproduction without express written consent39 This option works the same as the Amino Acid Constraints

40. VOCs: Ortholog Group Filter – Top Section Copyright OpenHelix. No use or reproduction without express written consent40 Top dropdown menus to select virus & gene of interest Use Ortholog Group Selector if you know something about the ortholog group you are searching for, i.e. ID or name

41. VOCs: Ortholog Group Filter – Lower Section Copyright OpenHelix. No use or reproduction without express written consent41 Select Click

42. VOCs: Genome Filter & Virus Selector Copyright OpenHelix. No use or reproduction without express written consent42 Click Final constraint tool

43. VOCs: Example Criteria Copyright OpenHelix. No use or reproduction without express written consent43 Click Our example: all Poxviridae genes within ortholog group 'Thymidine kinase' Scrol l

44. VOCs: Applying Constraints with Toolbar Buttons Copyright OpenHelix. No use or reproduction without express written consent44 Click

45. VOCs: Gene Results Table Copyright OpenHelix. No use or reproduction without express written consent45 You can highlight one or more gene entries and click on 'Display' to find out more about it Click

46. VOCs: Gene Data & Gene Notes Tabs Copyright OpenHelix. No use or reproduction without express written consent46 We will examine the 'DNA/aa Statistics' tab in the next slide

47. VOCs: DNA/aa Statistics Tab Copyright OpenHelix. No use or reproduction without express written consent47 Top Section Middle Section Lower Section

48. VOCs: 'Family' Button Copyright OpenHelix. No use or reproduction without express written consent48 Click This will display all genes that fall into the same Ortholog Group

49. VOCs: 'Sequences' Button Copyright OpenHelix. No use or reproduction without express written consent49 Click This will show color-coded DNA & protein sequences for the highlighted gene

50. VOCs: 'Notes' Button Copyright OpenHelix. No use or reproduction without express written consent50 Click This will open the same notes information as you find in the gene information table

51. Copyright OpenHelix. No use or reproduction without express written consent51 VBRC Agenda Introduction and Credits VBRC Resources Virus Orthologous Clusters (VOCs) VOCs Additional Features Additional Tools Summary Exercises VBRC: http://www.vbrc.orghttp://www.vbrc.org

52. VOCs: Column Options Copyright OpenHelix. No use or reproduction without express written consent52 Click

53. VOCs: GO Terms & InterPro Hits Copyright OpenHelix. No use or reproduction without express written consent53 Click

54. VOCs: PDB Structures Copyright OpenHelix. No use or reproduction without express written consent54 Click Enter Family & Dates

55. VOCs: Sequence Searcher Copyright OpenHelix. No use or reproduction without express written consent55 Click

56. VOCs: Sequence Searcher – Input Options Copyright OpenHelix. No use or reproduction without express written consent56 Click

57. VOCs: Sequence Searcher - Results Copyright OpenHelix. No use or reproduction without express written consent57

58. VOCs: Blast Copyright OpenHelix. No use or reproduction without express written consent58Copyright OpenHelix. No use or reproduction without express written consent58Copyright OpenHelix. No use or reproduction without express written consent58 Click

59. VOCs: Alignment CLICK Copyright OpenHelix. No use or reproduction without express written consent59

60. Base by Base Alignment Editor Copyright OpenHelix. No use or reproduction without express written consent60 Click Drag Click Color-coded bases & interactive sequences Results

61. Base by Base Alignment Editor – Menu Options Copyright OpenHelix. No use or reproduction without express written consent61

62. VOCs: Analysis Tools - Hydrophobicity Plot Copyright OpenHelix. No use or reproduction without express written consent62 Click

63. VOCs: Analysis Tools - DNA Grapher Copyright OpenHelix. No use or reproduction without express written consent63 Click

64. VOCs: JDotter Copyright OpenHelix. No use or reproduction without express written consent64 Click

65. Copyright OpenHelix. No use or reproduction without express written consent65 VBRC Agenda Introduction and Credits VBRC Resources Virus Orthologous Clusters (VOCs) VOCs Additional Features Additional Tools Summary Exercises VBRC: http://www.vbrc.orghttp://www.vbrc.org

66. Viral Genome Organizer (VGO) Copyright OpenHelix. No use or reproduction without express written consent66 JAVA-based, displays genome information such as genes, ORFs & start/stop codons http://athena.bioc.uvic.ca/coverflow

67. Genome Annotation Transfer Utility (GATU) Copyright OpenHelix. No use or reproduction without express written consent67 For genomes not as well characterized BLAST vs. a reference genome to add annotation eGATU – 'easy GATU', no reference needed

68. Genome-Based Fingerprint Scanning (GFS) Copyright OpenHelix. No use or reproduction without express written consent68 Identify proteins in genomes not well characterized from mass spectrometry data Comparison to a reference genome Easy & inexpensive method to identify proteins

69. Copyright OpenHelix. No use or reproduction without express written consent69 VBRC Agenda Introduction and Credits VBRC Resources Virus Orthologous Clusters (VOCs) VOCs Additional Features Additional Tools Summary Exercises VBRC: http://www.vbrc.orghttp://www.vbrc.org

70. Comprehensive, Updated & Freely Available Data Copyright OpenHelix. No use or reproduction without express written consent70 Curated sequence data Many resources & tools NIH/NIAID Category A, B & C priority pathogens

71. Copyright OpenHelix. No use or reproduction without express written consent71 VBRC Agenda Introduction and Credits VBRC Resources Virus Orthologous Clusters (VOCs) VOCs Additional Features Additional Tools Summary Exercises VBRC: http://www.vbrc.orghttp://www.vbrc.org

72. Copyright OpenHelix. No use or reproduction without express written consent72