2. Copyright OpenHelix. No use or reproduction without express written consent 2 Overview of Genome Browsers Materials prepared by Warren C. Lathe, Ph.D. Mary Mangan, Ph.D. Jennifer Williams, Ph.D. www.openhelix.com

3. Copyright OpenHelix. No use or reproduction without express written consent3 Genome Browsers Agenda Introduction Ensembl UCSC Genome Browser NCBI Map Viewer IMG: Integrated Microbial Genomes GBrowse Other Genome Browsers Summary Ensembl Genome Browser: http://www.ensembl.orghttp://www.ensembl.org UCSC Genome Browser: http://genome.ucsc.eduhttp://genome.ucsc.edu NCBI Map Viewer: http://ncbi.nlm.nih.gov/mapviewhttp://ncbi.nlm.nih.gov/mapview IMG: http://img.jgi.doe.govhttp://img.jgi.doe.gov GBrowse: http://gmod.org/wiki/Gbrowse

4. Copyright OpenHelix. No use or reproduction without express written consent4 Exponential Growth in Genomic Sequence Data Data from www.genomesonline.org & www.genomesonline.org http://www.ncbi.nlm.nih.gov/s ites/entrez?db=genomeprj # of genomes Nearly 3,000+ completed genomes Official “15 year” Human Genome Project: 1990-2003 First 2 bacterial genomes complete First eukaryote complete (yeast) First metazoan complete (flatworm)

5. Copyright OpenHelix. No use or reproduction without express written consent5 2000 : 230 databases and tools listed in compilation 1996 : first annual compilation of databases and tools lists 57 databases and tools The annual database issue of Nucleic Acids Research has grown exponentially 2006: 856 databases and tools listed in compilation A Concurrent Explosion in Databases & Tools 2011: 1330 databases and tools http://nar.oxfordjournals.org/content/vol38/suppl_1/index.dtl

6. Copyright OpenHelix. No use or reproduction without express written consent6 [Human] Genome Browsers Not limited to only human data EBI Ensembl NCBI Map Viewer UCSC Genome Browser

7. Copyright OpenHelix. No use or reproduction without express written consent7 IMG: Integrated Microbial Genomes IMG: http://img.jgi.doe.govhttp://img.jgi.doe.gov Currently over 6000 genomes Not limited to only microbial data

8. Copyright OpenHelix. No use or reproduction without express written consent8 GBrowse: Generic Genome Browser photo: NIH http://gmod.org/wiki/Gbrowse

9. Copyright OpenHelix. No use or reproduction without express written consent9 Genome Browsers Provide Context IMG EBI Ensembl NCBI Map Viewer UCSC Genome Browser GBrowse

10. Copyright OpenHelix. No use or reproduction without express written consent10 genes & predictions variations & repeats cross-species comparative data & many more types of data from expression & regulation to mRNA and ESTs… Gene X Description Transcript data Structure Gene Ontology Pathway Data Homologous Genes Expression Data Etc…. Organized Data Based on Chromosome Location tracks

11. Copyright OpenHelix. No use or reproduction without express written consent11 Genome Browsers Agenda Introduction Ensembl UCSC Genome Browser NCBI Map Viewer IMG: Integrated Microbial Genomes GBrowse Other Genome Browsers Summary Ensembl Genome Browser: http://www.ensembl.orghttp://www.ensembl.org UCSC Genome Browser: http://genome.ucsc.eduhttp://genome.ucsc.edu NCBI Map Viewer: http://ncbi.nlm.nih.gov/mapviewhttp://ncbi.nlm.nih.gov/mapview IMG: http://img.jgi.doe.govhttp://img.jgi.doe.gov GBrowse: http://gmod.org/wiki/Gbrowse

12. Copyright OpenHelix. No use or reproduction without express written consent12 Ensembl Homepage www.ensembl.org Click or here ↔ + BUILT, MAINTAINED, & FUNDED BY:

13. Copyright OpenHelix. No use or reproduction without express written consent13 Ensembl: An Example Jump to other browsers – UCSC & NCBI Click for more details tracks

14. Copyright OpenHelix. No use or reproduction without express written consent Ensembl: Many Additional Tools best scoring match BLAST/BLAT data retrieval and download BioMart

15. Other Ensembl Installations EnsemblMetazoa EnsemblPlants EnsemblFungi EnsemblProtists EnsemblBacteria Copyright OpenHelix. No use or reproduction without express written consent15 http://www.ensembl.org/info/about/species.html

16. Copyright OpenHelix. No use or reproduction without express written consent16 Genome Browsers Agenda Introduction Ensembl UCSC Genome Browser NCBI Map Viewer IMG: Integrated Microbial Genomes GBrowse Other Genome Browsers Summary Ensembl Genome Browser: http://www.ensembl.orghttp://www.ensembl.org UCSC Genome Browser: http://genome.ucsc.eduhttp://genome.ucsc.edu NCBI Map Viewer: http://ncbi.nlm.nih.gov/mapviewhttp://ncbi.nlm.nih.gov/mapview IMG: http://img.jgi.doe.govhttp://img.jgi.doe.gov GBrowse: http://gmod.org/wiki/Gbrowse

17. Copyright OpenHelix. No use or reproduction without express written consent17 UCSC Genome Browser Homepage http://genome.ucsc.edu Genome Bioinformatics Group (UCSC, University of California, Santa Cruz)

18. Copyright OpenHelix. No use or reproduction without express written consent18 UCSC Genome Browser Jump to Ensembl & NCBI Controls for top data tracks displayed are in lower page section Groups of Tracks Tracks Collapse/expand groups Groups of Tracks Track display controls tracks

19. Copyright OpenHelix. No use or reproduction without express written consent19 Many Tools & Options Available Get DNA, Customize Output Access to a tremendous amount of information! BLAT Search

20. UCSC Browser Other Installations Archaeal genomes Arabidopsis Malaria HIV Copyright OpenHelix. No use or reproduction without express written consent20

21. Copyright OpenHelix. No use or reproduction without express written consent21 Genome Browsers Agenda Introduction Ensembl UCSC Genome Browser NCBI Map Viewer IMG: Integrated Microbial Genomes GBrowse Other Genome Browsers Summary Ensembl Genome Browser: http://www.ensembl.orghttp://www.ensembl.org UCSC Genome Browser: http://genome.ucsc.eduhttp://genome.ucsc.edu NCBI Map Viewer: http://ncbi.nlm.nih.gov/mapviewhttp://ncbi.nlm.nih.gov/mapview IMG: http://img.jgi.doe.govhttp://img.jgi.doe.gov GBrowse: http://gmod.org/wiki/Gbrowse

22. Copyright OpenHelix. No use or reproduction without express written consent22 Map Viewer Homepage http://ncbi.nlm.nih.gov/mapview Select a species

23. Copyright OpenHelix. No use or reproduction without express written consent23 NCBI Map Viewer Browser Page Contig map Sequence map (UniGene) Sequence map (Genes_seq) Default Maps – easy to change Ideogram Scroll down to Summary of Maps

24. Copyright OpenHelix. No use or reproduction without express written consent24Copyright OpenHelix. No use or reproduction without express written consent24 Map Viewer Provides Many Tools & Options BLAST Searches Use Maps & Options to add/remove maps Advanced Searches Clone Finder

25. Copyright OpenHelix. No use or reproduction without express written consent25 Genome Browsers Agenda Introduction Ensembl UCSC Genome Browser NCBI Map Viewer IMG: Integrated Microbial Genomes GBrowse Other Genome Browsers Summary Ensembl Genome Browser: http://www.ensembl.orghttp://www.ensembl.org UCSC Genome Browser: http://genome.ucsc.eduhttp://genome.ucsc.edu NCBI Map Viewer: http://ncbi.nlm.nih.gov/mapviewhttp://ncbi.nlm.nih.gov/mapview IMG: http://img.jgi.doe.govhttp://img.jgi.doe.gov GBrowse: http://gmod.org/wiki/Gbrowse

26. Copyright OpenHelix. No use or reproduction without express written consent26 IMG: Integrated Microbial Genomes IMG: http://img.jgi.doe.govhttp://img.jgi.doe.gov Many species, but focus is microbial

27. Copyright OpenHelix. No use or reproduction without express written consent27 IMG Gene Report – Extensive & Detailed DNA Sequence Protein Sequence Pathway Map candidate enzyme or product name

28. Copyright OpenHelix. No use or reproduction without express written consent28 IMG Gene Report – Evidence of Functions orthologs domains

29. Copyright OpenHelix. No use or reproduction without express written consent29Copyright OpenHelix. No use or reproduction without express written consent29 IMG Gene Report: Many Tools & Links IMG BLAST form IMG phylogenetic search Homology Toolkit Use MyIMG to: Upload a set of Genomes, Set Search Preferences, Upload Gene Annotations MyIMG

30. Copyright OpenHelix. No use or reproduction without express written consent30 Genome Browsers Agenda Introduction Ensembl UCSC Genome Browser NCBI Map Viewer IMG: Integrated Microbial Genomes GBrowse Other Genome Browsers Summary Ensembl Genome Browser: http://www.ensembl.orghttp://www.ensembl.org UCSC Genome Browser: http://genome.ucsc.eduhttp://genome.ucsc.edu NCBI Map Viewer: http://ncbi.nlm.nih.gov/mapviewhttp://ncbi.nlm.nih.gov/mapview IMG: http://img.jgi.doe.govhttp://img.jgi.doe.gov GBrowse: http://gmod.org/wiki/Gbrowse

31. Copyright OpenHelix. No use or reproduction without express written consent31 GBrowse: Generic Genome Browser http://gmod.org/wiki/Gbrowse GBrowse - developed by GMOD Generic Model Organism Database - web application to explore genomes - free software - goal: simplify & standardize MOD Model Organism Databases http://genome.cshlp.org/content/12/10/1599.long Popular

32. Copyright OpenHelix. No use or reproduction without express written consent32Copyright OpenHelix. No use or reproduction without express written consent32 GBrowse: a Popular Viewer Human Genome Segmental Duplication Database bird’s eye view......or zoom in for details customize it colored glyphs (icons)

33. Copyright OpenHelix. No use or reproduction without express written consent33Copyright OpenHelix. No use or reproduction without express written consent33 GBrowse: Both Universal & Unique U N I V E R S A L A P P E A R A N C E U N I Q U E A P P E A R A N C E Tracks Learn GBrowse once – use it everywhere! Customize your view

34. Copyright OpenHelix. No use or reproduction without express written consent34 WebGBrowse & JBrowse http://webgbrowse.cgb.indiana.edu/webgbrowse/cgi-bin/uploadData Additional Options http://gmod.org/wiki/JBrowse

35. Copyright OpenHelix. No use or reproduction without express written consent35 Genome Browsers Agenda Introduction Ensembl UCSC Genome Browser NCBI Map Viewer IMG: Integrated Microbial Genomes GBrowse Other Genome Browsers Summary Ensembl Genome Browser: http://www.ensembl.orghttp://www.ensembl.org UCSC Genome Browser: http://genome.ucsc.eduhttp://genome.ucsc.edu NCBI Map Viewer: http://ncbi.nlm.nih.gov/mapviewhttp://ncbi.nlm.nih.gov/mapview IMG: http://img.jgi.doe.govhttp://img.jgi.doe.gov GBrowse: http://gmod.org/wiki/Gbrowse

36. Copyright OpenHelix. No use or reproduction without express written consent36 IGV: Integrative Genomics Viewer IGV: http://www.broadinstitute.org/igv/ Datasets & Genomes available

37. Copyright OpenHelix. No use or reproduction without express written consent37 Many Additional Genome Browsers Available ARGO: http://www.broadinstitute.org/annotation/argo/ IGB: http://igb.bioviz.org/ CGView: http://wishart.biology.ualberta.ca/cgview/ Gaggle: http://gaggle.systemsbiology.n et/docs/geese/genomebrowser/

38. Copyright OpenHelix. No use or reproduction without express written consent38 Genome Browsers Agenda Introduction Ensembl UCSC Genome Browser NCBI Map Viewer IMG: Integrated Microbial Genomes GBrowse Other Genome Browsers Summary Ensembl Genome Browser: http://www.ensembl.orghttp://www.ensembl.org UCSC Genome Browser: http://genome.ucsc.eduhttp://genome.ucsc.edu NCBI Map Viewer: http://ncbi.nlm.nih.gov/mapviewhttp://ncbi.nlm.nih.gov/mapview IMG: http://img.jgi.doe.govhttp://img.jgi.doe.gov GBrowse: http://gmod.org/wiki/Gbrowse

39. Copyright OpenHelix. No use or reproduction without express written consent39 Genome Browsers - Similarities & Differences IMG EBI Ensembl NCBI Map Viewer UCSC Genome Browser GBrowse

40. Copyright OpenHelix. No use or reproduction without express written consent40 Summary of These Genome Browsers Chromosome orientation Species totals Oct 2011 Human Genome Oct 2011 Custom track tool Custom query tool Sequence search Ensembl (main site) horizontal58GRCh37DASBioMartBLAST or BLAT NCBI Map Viewer vertical123NCBI build 37.1 BLAST UCSC Genome Browser horizontal53GRCh37Custom Tracks Table Browser BLAT IMGlinear/ horizontal 6000+YesIMG Annotation Site My IMGBLAST GBrowsehorizontal100+ at different sites variousDASBLAST

41. Copyright OpenHelix. No use or reproduction without express written consent41 Compare & Contrast of These Genome Browsers Organisms included (example of focus) Restriction enzyme data Search for locations by protein domain Search for overlap in datasets Sort genes by chosen criteria Sequence similarity search on multiple species Ensembl (main site) mostly vertebrate Yes Restricted: BioMart Yes NCBI Map Viewer Range; plant, fungi, insects, vertebrate No My NCBI Restricted: Selected groups UCSC Genome Browser vertebrate, insect, model organisms, others YesRestricted Table Browser Yes: Table Browser Gene Sorter No IMGAll Microbes, 16 model eukaryotes NoYesPhylo- genetically Some options Yes GBrowseVaries by individual implementation at different sites

42. Copyright OpenHelix. No use or reproduction without express written consent42 GBrowse & Newer Genome Browsers photo: NIH Basis of so many browsers GBrowse Many Newer Browsers

43. Copyright OpenHelix. No use or reproduction without express written consent43 OpenHelix Tutorials Available for Many Browsers More detail on software functionality Exercises and slides Free provider-sponsored materials: www.openhelix.com