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

2. NCBI Viral Genomes The NCBI Viral Genomes Resource Materials prepared by: Jennifer Williams, Ph.D. www.openhelix.com Updated: Q2 2011 Version 2.0

3. Copyright OpenHelix. No use or reproduction without express written consent3 NCBI Viral Genomes Agenda Introduction & Credits Basic Search Tools: BLAST & PASC Tools: Protein Clusters Other Features Summary Exercises NCBI Viral Genomes: http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=10239

4. Copyright OpenHelix. No use or reproduction without express written consent4 Introduction NCBI Viral Genomes Part of the NCBI Entrez-Genome collection Establishes a reference sequence for each viral genome Organizes data by taxonomy Provides tools to compare & analyze viral sequences Integrated with NCBI’s other databases

5. Copyright OpenHelix. No use or reproduction without express written consent5 The Discovery of Viruses still toxic FILTER removes bacteria Dimitri Ivanovski diseased tobacco leaves Martinus Beijerinck tobacco mosaic virus agent = poison “VIRUS” ( Latin )

6. Copyright OpenHelix. No use or reproduction without express written consent6 The Importance of Viruses MEDICAL AIDS Ebola Cancer Influenza Bio-terrorism AGRICULTURAL Wheat Mosaic Corn Necrosis Soybean Mosaic Tomato Wilt Agri-terrorism A virus infects a host cell. Replicates its genome & coat. Then breaks free to infect new cells.

7. Copyright OpenHelix. No use or reproduction without express written consent7 Managing Viral Genome Sequences HIV-1 250,000+ records... Reference Sequence NC_001802...reduced to one Reference Sequence Viral Sequences NCBI Viral Genomes

8. Copyright OpenHelix. No use or reproduction without express written consent8 NCBI Viral Genomes Preview Taxonomy RefSeq Genome Summary GenBank PubMed

9. Copyright OpenHelix. No use or reproduction without express written consent9 NCBI Viral Genomes Homepage Navigation

10. Copyright OpenHelix. No use or reproduction without express written consent10 NCBI Viral Genomes Agenda Introduction & Credits Basic Search Tools: BLAST & PASC Tools: Protein Clusters Other Features Summary Exercises NCBI Viral Genomes: http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=10239

11. Copyright OpenHelix. No use or reproduction without express written consent11 Search for a Virus: Complete List of Genomes Scroll down Sort genomes by:Filter by host Download

12. Copyright OpenHelix. No use or reproduction without express written consent12 Search for a Virus: via Taxonomy Pick-list Select taxon

13. 13 Search for a Virus: via Entrez-Genome Apple chlorotic leaf spot virus Search Results Overview display Genome sequences for all viruses in taxon Copyright OpenHelix. No use or reproduction without express written consent

14. 14 Measles Virus Click Genome name RefSeq accession ID LengthProteins Genome neighbors Host & dates Source Copyright OpenHelix. No use or reproduction without express written consent

15. Nucleotides 15 Measles Virus: Taxonomy Structure PubMed Central Copyright OpenHelix. No use or reproduction without express written consent

16. 16 Measles Virus: Accession ID GenBank Click Overview display Entrez Gene Genome ProjectPubMed Sequence Viewer

17. Copyright OpenHelix. No use or reproduction without express written consent17 Measles Virus: Proteins Protein length histogram Entrez Protein Entrez Gene

18. Copyright OpenHelix. No use or reproduction without express written consent18 Measles Virus: Genome Neighbors Reference sequence Genome neighbors Sequence differences are color-coded Sequence difference histogram

19. Copyright OpenHelix. No use or reproduction without express written consent19 NCBI Viral Genomes Agenda Introduction & Credits Basic Search Tools: BLAST & PASC Tools: Protein Clusters Other Features Summary Exercises NCBI Viral Genomes: http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=10239

20. Copyright OpenHelix. No use or reproduction without express written consent20 Viral Genomes Tools

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

22. Copyright OpenHelix. No use or reproduction without express written consent22 PASC - Pairwise Sequence Comparison

23. Copyright OpenHelix. No use or reproduction without express written consent23 Viral genomes used for PASC PASC: Families

24. Copyright OpenHelix. No use or reproduction without express written consent24 Percent Identity (0 to 100%) ~ 400 comparisons with ~ 58% identity Click on bar for details Highly similar viruses # Viral Comparisons Key PASC: Histogram for Alphaflexiviridae

25. PASC: Histogram Details Copyright OpenHelix. No use or reproduction without express written consent25

26. Copyright OpenHelix. No use or reproduction without express written consent26 NC_001554 TIP: completed viral genomes only! PASC: Upload a Viral Genome for Comparison

27. Copyright OpenHelix. No use or reproduction without express written consent27 Scroll down Input sequence shares ~ 46% PASC: Query Results

28. Copyright OpenHelix. No use or reproduction without express written consent28 Input sequence Best matches PASC: Top 15 Matches from Query % identity

29. Copyright OpenHelix. No use or reproduction without express written consent29 NCBI Viral Genomes Agenda Introduction & Credits Basic Search Tools: BLAST & PASC Tools: Protein Clusters Other Features Summary Exercises NCBI Viral Genomes: http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=10239

30. Copyright OpenHelix. No use or reproduction without express written consent30 5 classes of viruses 4 resources 1 Protein Clusters Homepage Note

31. Copyright OpenHelix. No use or reproduction without express written consent31 ABCDEFGHIJABCDEFGHIJ VOG: Clusters List

32. Copyright OpenHelix. No use or reproduction without express written consent32 Click VOG: Clusters List: Adenoviridae

33. Copyright OpenHelix. No use or reproduction without express written consent33 VOG: Detail Page

34. Copyright OpenHelix. No use or reproduction without express written consent34 VOG: Function Resource 2

35. Copyright OpenHelix. No use or reproduction without express written consent35 Click VOG: Functional Categories

36. Copyright OpenHelix. No use or reproduction without express written consent36 Family # Proteins VOG function VOG: Function: Regulation of Cellular Metabolism

37. Copyright OpenHelix. No use or reproduction without express written consent37 3 VOG: CDD Resource

38. Copyright OpenHelix. No use or reproduction without express written consent38 Click to sort table VOG: CDD Results

39. Copyright OpenHelix. No use or reproduction without express written consent39 4 VOG: BLAST Resource

40. Copyright OpenHelix. No use or reproduction without express written consent40 9633655 Click VOG: BLAST Query

41. Copyright OpenHelix. No use or reproduction without express written consent41 VOG: BLAST Results

42. Copyright OpenHelix. No use or reproduction without express written consent42 9626445 Protein found Associated VOG Other VOG members Virus class VOG: Search From Protein Clusters Homepage VOG search box

43. Copyright OpenHelix. No use or reproduction without express written consent43 VOG: by Taxonomy Groups Click

44. Copyright OpenHelix. No use or reproduction without express written consent44 NCBI Viral Genomes Agenda NCBI Viral Genomes: http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=10239 Introduction & Credits Basic Search Tools: BLAST & PASC Tools: Protein Clusters Other Features Summary Exercises

45. Copyright OpenHelix. No use or reproduction without express written consent45 Homepage Navigation Bar

46. Copyright OpenHelix. No use or reproduction without express written consent46 Citation, FAQs & Help

47. Copyright OpenHelix. No use or reproduction without express written consent47 Select best matches virus A best matches virus B Genotyping Click on example

48. Copyright OpenHelix. No use or reproduction without express written consent48 Influenza Virus Resource

49. Copyright OpenHelix. No use or reproduction without express written consent49 SARS Resource

50. Copyright OpenHelix. No use or reproduction without express written consent50 Non-NCBI Virus Databases

51. Copyright OpenHelix. No use or reproduction without express written consent51 Related Sites

52. Copyright OpenHelix. No use or reproduction without express written consent52 NCBI Viral Genomes Agenda NCBI Viral Genomes: http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=10239 Introduction & Credits Basic Search Tools: BLAST & PASC Tools: Protein Clusters Other Features Summary Exercises

53. Copyright OpenHelix. No use or reproduction without express written consent53 1 Reference Sequence Thousands of Viral Sequences ~ 400,000 sequences for HIV-1 1 RefSeq (NC_001802) Raw Data Molecular Standard NCBI Viral Genomes: Reduces Complexity NCBI Viral Genomes

54. Copyright OpenHelix. No use or reproduction without express written consent54 Viral Genomes: Integrated with NCBI Resources Taxonomy RefSeq Genome Summary GenBank PubMed

55. Copyright OpenHelix. No use or reproduction without express written consent55 Compare virus identities Explore virus protein clusters Add your own data for analysis & comparison NCBI Viral Genomes: Tools

56. Copyright OpenHelix. No use or reproduction without express written consent56 Other NCBI virus-specific databases Non-NCBI virus databases History & photos of viruses NCBI Viral Genomes: Numerous Link-Outs

57. Copyright OpenHelix. No use or reproduction without express written consent57 NCBI Viral Genomes Agenda NCBI Viral Genomes: http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=10239 Introduction & Credits Basic Search Tools: BLAST & PASC Tools: Protein Clusters Other Features Summary Exercises

58. Copyright OpenHelix. No use or reproduction without express written consent58