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

2. Integrated Microbial Genomes by the DOE Joint Genome Institute A public resource for the comparative analysis of genomes Materials prepared by: Erica Balzer, Ph.D. Jennifer Williams, Ph.D. www.openhelix.com Updated Q4 2010 Version 12

3. Copyright OpenHelix. No use or reproduction without express written consent3 IMG Agenda Introduction and Credits Find and Examine Genomes Find and Examine Genes Find and Examine Functions Compare Genomes Analysis Carts MyIMG Summary Exercises Integrated Microbial Genomes: http://img.jgi.doe.govhttp://img.jgi.doe.gov

4. Copyright OpenHelix. No use or reproduction without express written consent4 IMG Homepage http://img.jgi.doe.gov/cgi-bin/pub/main.cgi currently over 6000 genomes next release

5. Copyright OpenHelix. No use or reproduction without express written consent5 IMG Announcements Important Computer Requirements Firefox 3.6, Internet Explorer 8 Microsoft Windows XP SP2 or later, Macintosh OS X 10.4 or above, or Linux Modern Intel or AMD CPU At least 1.0 GB RAM JavaScript and Cookies must enabled Java 1.6 Release notes click

6. Copyright OpenHelix. No use or reproduction without express written consent6 Credits for the Integrated Microbial Genomes (IMG) system http://img.jgi.doe.gov/pub/doc/credits.html http://img.jgi.doe.gov/pub/doc/datasources.html “This work was performed under the auspices of the U.S. Department of Energy, Office of Biological and Environmental Research; the University of California; and Lawrence Berkeley, Lawrence Livermore, and Los Alamos National Laboratories”

7. Copyright OpenHelix. No use or reproduction without express written consent7 Integrated Microbial Genome Content Sequence Information Domain & Family Info Function Info Pathway Info http://img.jgi.doe.gov/pub/doc/datamodel.html Enzyme Info Ortholog Info Taxonomic Information

8. Copyright OpenHelix. No use or reproduction without express written consent8 Integrated Microbial Genome Publication http://nar.oxfordjournals.org/cgi/reprint/gkp887v1

9. Copyright OpenHelix. No use or reproduction without express written consent9 Introductory IMG Tutorial Content Typical Analysis: 1. Find a set of objects (genomes, genes, or functions) 2. Analyze profiles of objects (with regards to other object types) Combine functions to create powerful analyses http://img.jgi.doe.gov/pub/doc/images/uiMap.pdf

10. Copyright OpenHelix. No use or reproduction without express written consent10 IMG Help & Documentation

11. IMG Statistics Copyright OpenHelix. No use or reproduction without express written consent11 Domain name, # of genomes, gene counts, % total count Cluster stats Function stats Pathway stats Experiment stats

12. Project Map & Content History Copyright OpenHelix. No use or reproduction without express written consent12

13. Copyright OpenHelix. No use or reproduction without express written consent13 IMG Agenda Introduction and Credits Find and Examine Genomes Find and Examine Genes Find and Examine Functions Compare Genomes Analysis Carts MyIMG Summary Exercises Integrated Microbial Genomes: http://img.jgi.doe.govhttp://img.jgi.doe.gov Introduction and Credits

14. Copyright OpenHelix. No use or reproduction without express written consent14 DOE Joint Genome Institute Copyright OpenHelix. No use or reproduction without express written consent http://www.jgi.doe.gov/

15. Copyright OpenHelix. No use or reproduction without express written consent15 Finding Genomes from Homepage click any link to select that subset of genomes text search to find genomes of interest http://img.jgi.doe.gov/ search genomes by metadata categories click here for full list of associated genomes

16. Copyright OpenHelix. No use or reproduction without express written consent16 Finding Genomes by Browsing deselect species by clicking switch to phylogeny display

17. Copyright OpenHelix. No use or reproduction without express written consent17 Select Species by Phylogeny Green dot to select, Red dot to clear

18. Copyright OpenHelix. No use or reproduction without express written consent18 Genome Search Search by Metadata Categories

19. Copyright OpenHelix. No use or reproduction without express written consent Genome Search by Categories 19 Assignments from GOLD, include: Cell Shape, Disease, Habitat, Host Name, etc. Phenotype Select “Acidophile” Phenotype = acidophile OR algicidal AND Metabolism = auxotroph

20. Copyright OpenHelix. No use or reproduction without express written consent20 Genome Category Search Results Saved all acidophile genomes click

21. Copyright OpenHelix. No use or reproduction without express written consent21 Organism Details Report: Overview Organism Information Genome Statistics Details Reports Provide: * Detailed Information * Statistical Summaries * Analysis Tools * And more for genomes, genes, and functions Comparative Analysis Functions Download & Export

22. Copyright OpenHelix. No use or reproduction without express written consent22 Organism Details Report: Information Name taxonomy details sequence links sequence details metadata

23. Copyright OpenHelix. No use or reproduction without express written consent23 Organism Details Report: Statistics sequence scaffolds gene counts clusters

24. Organism Details Report: Phylogenetic Distribution of Genes Copyright OpenHelix. No use or reproduction without express written consent24 Gene list Family info

25. Organism Details Report: Putative Horizontally Transferred Genes Copyright OpenHelix. No use or reproduction without express written consent25 Origin of horizontal transfer

26. Copyright OpenHelix. No use or reproduction without express written consent26 Organism Details Report: Viewers

27. Copyright OpenHelix. No use or reproduction without express written consent27 Organism Details Report: Annotations gene one gene two

28. Copyright OpenHelix. No use or reproduction without express written consent28 Organism Details Report: Download & Export

29. Copyright OpenHelix. No use or reproduction without express written consent29 IMG Agenda Introduction and Credits Find and Examine Genomes Find and Examine Genes Find and Examine Functions Compare Genomes Analysis Carts MyIMG Summary Exercises Integrated Microbial Genomes: http://img.jgi.doe.govhttp://img.jgi.doe.gov Introduction and Credits

30. Copyright OpenHelix. No use or reproduction without express written consent30 Keyword Gene Search & Cassette Search Keyword Search Form keyword filters genomes filters Cassette Search Form Search Text filters genomes

31. Copyright OpenHelix. No use or reproduction without express written consent31 Phylogenetic Profiler Gene Search with homologs in but no homologs in find genes in and don’t search in the rest Similarity Cutoffs Phylogenetic Profile Search Form

32. Copyright OpenHelix. No use or reproduction without express written consent32 Phylogenetic Profiler Results Missing Gene? highlights genes that don’t have homologs in other genomes

33. Copyright OpenHelix. No use or reproduction without express written consent33 Sequence Similarity Gene Search Enter Sequence Select Genome Set

34. Copyright OpenHelix. No use or reproduction without express written consent34 BLAST Query Report best hits alignments query stats open gene report

35. Copyright OpenHelix. No use or reproduction without express written consent35 IMG Gene Report: Overview for Gene ID 637421235 gene information Gene Details Evidence of Function & Structure Tools, Links & Homologs protein information pathway information COG matches Pfam matches similarity tools gene neighborhood navigation links Find Genes Tab Gene Search submenu 637421235 IMG Gene Object Identifier

36. Copyright OpenHelix. No use or reproduction without express written consent36 IMG Gene Report: Gene Details DNA Sequence Protein Sequence Pathway Map candidate enzyme or product name

37. Copyright OpenHelix. No use or reproduction without express written consent37 IMG Gene Report: Evidence of Functions Orthologs Domains chromosome view ortholog neighborhoods

38. NCBI BLAST form Copyright OpenHelix. No use or reproduction without express written consent38 IMG Gene Report: Tools & Links IMG BLAST form IMG phylogenetic search in this species PDB BLAST form InterPro Scan

39. Copyright OpenHelix. No use or reproduction without express written consent39 IMG Gene Report: Homology

40. Copyright OpenHelix. No use or reproduction without express written consent40 IMG Gene Report: Homologs Report click to add gene to gene cart sort by clicking any column headers dark grey indicates current sorting

41. Copyright OpenHelix. No use or reproduction without express written consent41 IMG Agenda Introduction and Credits Find and Examine Genomes Find and Examine Genes Find and Examine Functions Compare Genomes Analysis Carts MyIMG Summary Exercises Integrated Microbial Genomes: http://img.jgi.doe.govhttp://img.jgi.doe.gov Introduction and Credits

42. Copyright OpenHelix. No use or reproduction without express written consent42 Keyword Functions Search search examples search filters limit species hints

43. Copyright OpenHelix. No use or reproduction without express written consent43 Functional Alignment Search thymidylate kinase Enter keyword: thymidylate kinase Functional alignment results

44. Copyright OpenHelix. No use or reproduction without express written consent44 Browse for Functions IMG-specific qualifiers allow: * efficient functional annotation of genes * reliable genome comparison * confident reconstruction of the metabolic capabilities of the organisms And are applied manually by JGI and ORNL experts http://img.jgi.doe.gov/pub/doc/imgterms.html

45. Copyright OpenHelix. No use or reproduction without express written consent45 IMG Agenda Introduction and Credits Find and Examine Genomes Find and Examine Genes Find and Examine Functions Compare Genomes Analysis Carts MyIMG Summary Exercises Integrated Microbial Genomes: http://img.jgi.doe.govhttp://img.jgi.doe.gov Introduction and Credits

46. Saved all acidophile genomes Copyright OpenHelix. No use or reproduction without express written consent46 Comparing Genomes

47. genome statistics for the entire group of saved genomes Copyright OpenHelix. No use or reproduction without express written consent47 Group Statistics Individual genome statistics

48. Copyright OpenHelix. No use or reproduction without express written consent48 Genome Statistics Genome Table: Includes selected, genome-specific information Configuration Options: Choose from many types of information to customize table Output to Excel Refresh Report

49. Copyright OpenHelix. No use or reproduction without express written consent49 Other Comparative Genomics Tools Synteny Viewers: VISTA, Dotplot, Artemis, ACT Abundance Profiles: compare genomes by their functional profiles Genome Clustering: high level view of similarity among genomes Function Profile: find genes associated with a particular function Distance Tree: compare genomes by their functional profiles

50. Copyright OpenHelix. No use or reproduction without express written consent50 Synteny Viewers - VISTA species Alignments Species List http://genome.lbl.gov/vista

51. Distance Tree Copyright OpenHelix. No use or reproduction without express written consent51 Phylogenetic Distance Tree by Archaeopteryx applet options save

52. Copyright OpenHelix. No use or reproduction without express written consent Abundance Profile Viewer function family normalization species keyword Abundance Profile heat map 52

53. Copyright OpenHelix. No use or reproduction without express written consent53 Abundance Profile Search function family normalization species keyword Abundance Profile search result

54. Copyright OpenHelix. No use or reproduction without express written consent54 Function Profile Functions Genomes

55. Copyright OpenHelix. No use or reproduction without express written consent55 Genome Clustering Tools Hierarchical PCA Correlation Matrix

56. Copyright OpenHelix. No use or reproduction without express written consent56 IMG Agenda Introduction and Credits Find and Examine Genomes Find and Examine Genes Find and Examine Functions Compare Genomes Analysis Carts MyIMG Summary Exercises Integrated Microbial Genomes: http://img.jgi.doe.govhttp://img.jgi.doe.gov Introduction and Credits

57. Copyright OpenHelix. No use or reproduction without express written consent57 Genes Saved to Gene Cart

58. Copyright OpenHelix. No use or reproduction without express written consent58 Gene Cart Overview Gene Cart Functions: Select Genes Upload & Export Genes Comparison tools: Chromosome maps Sequence Alignments Gene Neighborhoods Profile Tools: Genome Filter Gene Profile Occurrence Profiles Function Alignment

59. Copyright OpenHelix. No use or reproduction without express written consent59 Export Gene Information my_gene_cart_genes.txt FASTA sequence

60. Copyright OpenHelix. No use or reproduction without express written consent60 Gene Comparison Tools specify display bands Map of chromosome

61. Copyright OpenHelix. No use or reproduction without express written consent61 Sequence Alignments ClustalW JalView

62. Filter for desired genomes Copyright OpenHelix. No use or reproduction without express written consent62 Gene Profile Analyses Genes vs. Genomes Genomes vs. Genes Occurrence Profile Saw earlier

63. Copyright OpenHelix. No use or reproduction without express written consent63 Function & Scaffold Carts Function Cart Functions: Can include COGs, Pfam, KEGG, enzymes, TIGR families, IMG Terms, etc. Select Functions Upload & Export Functions View Function Profile View Occurrence Profiles Additional Analysis Carts similar to Gene Analysis Cart Add to Scaffold Cart

64. Copyright OpenHelix. No use or reproduction without express written consent64 IMG Agenda Introduction and Credits Find and Examine Genomes Find and Examine Genes Find and Examine Functions Compare Genomes Analysis Carts MyIMG Summary Exercises Integrated Microbial Genomes: http://img.jgi.doe.govhttp://img.jgi.doe.gov Introduction and Credits

65. Copyright OpenHelix. No use or reproduction without express written consent65 MyIMG MyIMG allows you to: - Upload a set of Genomes - Set Search Preferences - Upload Gene Annotations

66. Copyright OpenHelix. No use or reproduction without express written consent66 IMG Agenda Introduction and Credits Find and Examine Genomes Find and Examine Genes Find and Examine Functions Compare Genomes Analysis Carts MyIMG Summary Exercises Integrated Microbial Genomes: http://img.jgi.doe.govhttp://img.jgi.doe.gov Introduction and Credits

67. Copyright OpenHelix. No use or reproduction without express written consent67 Summary http://img.jgi.doe.gov/ biological functions metabolic pathways genomes containing function of interest

68. Copyright OpenHelix. No use or reproduction without express written consent68 IMG Agenda Introduction and Credits Find and Examine Genomes Find and Examine Genes Find and Examine Functions Compare Genomes Analysis Carts MyIMG Summary Exercises Integrated Microbial Genomes: http://img.jgi.doe.govhttp://img.jgi.doe.gov Introduction and Credits

69. Copyright OpenHelix. No use or reproduction without express written consent69