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

2. UCSC Archaeal Genome Browser Materials prepared by: Cynthia Perreault-Micale, Ph.D. www.openhelix.com Updated: Q3 2010 Version 1.0

3. Copyright OpenHelix. No use or reproduction without express written consent3 UCSC Archaeal Genome Browser Agenda Introduction & Credits Basic Browsing & Searching Species-Specific Gateway Display Advanced Techniques Sequence Searching Summary Exercises UCSC Archaeal Genome Browser: http://archaea.ucsc.edu/

4. Copyright OpenHelix. No use or reproduction without express written consent4 Archaea – First Discovered in Extreme Environments Pictures from: http://en.wikipedia.org/wiki/Archaea Hot temperatures are not a problem Thriving in acid mine drainage Broad habitat, many in ocean Biotech, green chemistry, food processing, sewage treatment, antibiotics, evolution Their own domain, but may be more similar to eukaryotes than bacteria Imagine the unique biochemistry needed for survival

5. Copyright OpenHelix. No use or reproduction without express written consent5 Many Species, Powerful Genome Visualization Visualize the genomes of more than 50 Archaeal species Customizable, linked, access to additional tools & help Tools G/C content, EST sequences, IMG genes, Operon and EasyGene predictions, and more! Controls Search Click on features for more details

6. Copyright OpenHelix. No use or reproduction without express written consent6 Detailed & Extensive Annotation Tracks Data tracks are genome annotation Organized by grouping similar tracks Customizable, many options Tracks can differ between species And over time Updated frequently Groups Tracks Options Tracks can differ between species

7. Copyright OpenHelix. No use or reproduction without express written consent7 Homepage – Background & Help Help & Info http://archaea.ucsc.edu/

8. Copyright OpenHelix. No use or reproduction without express written consent8 Easy Access Abbreviations defined Click on any species to access genome browser homepage Search from here

9. Copyright OpenHelix. No use or reproduction without express written consent9 Credits

10. Copyright OpenHelix. No use or reproduction without express written consent10 Publications & Funding Funding http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D407 Data represent a collaborative effort

11. Copyright OpenHelix. No use or reproduction without express written consent11 UCSC Archaeal Genome Browser Agenda UCSC Archaeal Genome Browser: http://archaea.ucsc.edu/ Introduction & Credits Basic Browsing & Searching Species-Specific Gateway Display Advanced Techniques Sequence Searching Summary Exercises

12. Homepage – Getting Started 1. Click on any species in tree 2. Choose from a list of species 3. Select from menu organized by phyla 4. Use genome search box Copyright OpenHelix. No use or reproduction without express written consent12 http://archaea.ucsc.edu/ 1 1 2 2 3 4

13. 1 Copyright OpenHelix. No use or reproduction without express written consent13 Option 1 - Phylogeny Tree http://archaea.ucsc.edu/ Click on any species to reach their Genome Browser homepage

14. 2 Copyright OpenHelix. No use or reproduction without express written consent14 Option 2 - Select From List http://archaea.ucsc.edu/ Click on any species to reach their Genome Browser homepage

15. Copyright OpenHelix. No use or reproduction without express written consent15 Option 3 - Pull-down Menus http://archaea.ucsc.edu/ 3 Click here to open

16. Copyright OpenHelix. No use or reproduction without express written consent16 Option 3 - Menus on Individual Browser Pages Just select the clade and genome from dropdown menus Many query types accepted here

17. Copyright OpenHelix. No use or reproduction without express written consent17 Option 4 - Search Box http://archaea.ucsc.edu/ 4 Examples Pyro Select Click here

18. Copyright OpenHelix. No use or reproduction without express written consent18 An Example – Navigation Between Browser Pages We will go to the Pyrobaculum aerophilium Gateway page

19. Copyright OpenHelix. No use or reproduction without express written consent19 UCSC Archaeal Genome Browser Agenda UCSC Archaeal Genome Browser: http://archaea.ucsc.edu/ Introduction & Credits Basic Browsing & Searching Species-Specific Gateway Display Advanced Techniques Sequence Searching Summary Exercises

20. Search tools Species info, sequence, browse gene features Query examples Phylogenetic tree Copyright OpenHelix. No use or reproduction without express written consent20 Genome Browser Gateway A Gateway page for all genomes, use it to search or browse Your selected features, linked to browser

21. Copyright OpenHelix. No use or reproduction without express written consent21 Specific Genes/Features Click Examine CRISPR loci

22. Copyright OpenHelix. No use or reproduction without express written consent22 Sample Queries & Help Search tools Query examples Query examples to enter here Browse entire genome or Entrez Nucleotide entry

23. Copyright OpenHelix. No use or reproduction without express written consent23 Our Search Example - Helicase Browser uses cookies to remember your preferences Use the “Click here to reset” selection to return to default Example: helicases in the Pyrobaculum aerophilium genome

24. Copyright OpenHelix. No use or reproduction without express written consent24 Many Search Results for “Helicase” Categorized results list returned If only one hit, you will be taken directly to view it in browser Hits may correspond to overlapping regions Click here

25. Copyright OpenHelix. No use or reproduction without express written consent25 Genome Browser - Overview position/search box, image controls, visual display of features, links Annotation tracks, customization options, focus of next section Tools Controls Walk 95%, 45% or 10% to left or right Zoom Zoom to see individual bases Visual cues - direction of transcription

26. Copyright OpenHelix. No use or reproduction without express written consent26 Browser Basics – More Features & Options Click on features for details Even more data Click for track info & options And link to more information Save image to print or edit

27. Copyright OpenHelix. No use or reproduction without express written consent27 Browser Basics – Lower Data Tracks Terminators BlastP hits to Crenarchaea Comparative Genomics To Euryarchaea To other archaea To viruses & bacteria Click to toggle display density

28. Copyright OpenHelix. No use or reproduction without express written consent28 UCSC Archaeal Genome Browser Agenda UCSC Archaeal Genome Browser: http://archaea.ucsc.edu/ Introduction & Credits Basic Browsing & Searching Species-Specific Gateway Display Advanced Techniques Sequence Searching Summary Exercises

29. Copyright OpenHelix. No use or reproduction without express written consent29 Many Advanced Techniques & Help Are Available Advanced help exists already

30. Copyright OpenHelix. No use or reproduction without express written consent30 Manipulating Data Tracks Options Grouping Tracks Menu selections and defaults will vary Hide group To change track select option & click refresh

31. Copyright OpenHelix. No use or reproduction without express written consent31 Configuring Tracks Image width & text size Customize here, defaults are checked

32. Copyright OpenHelix. No use or reproduction without express written consent32 Retrieve & Format DNA Sequences Highlight by case, underline, bold, italic, add color

33. Copyright OpenHelix. No use or reproduction without express written consent33 Table Browser – Obtain Track Data in Text Format Follow links to help, tutorial & descriptions Use Table Browser to: Construct custom queries Obtain data in text format Calculate intersections between tracks Retrieve DNA associated w/ specific tracks

34. Copyright OpenHelix. No use or reproduction without express written consent34 UCSC Archaeal Genome Browser Agenda UCSC Archaeal Genome Browser: http://archaea.ucsc.edu/ Introduction & Credits Basic Browsing & Searching Species-Specific Gateway Display Advanced Techniques Sequence Searching Summary Exercises

35. Copyright OpenHelix. No use or reproduction without express written consent35 BLAT for Sequence Searching – Info & Access BLAT: BLAST-like Alignment Tool Speed & capacity advantages Locate sequence in genome or examine exon structure of mRNA http://genome.cshlp.org/content/12/4/656.long

36. Copyright OpenHelix. No use or reproduction without express written consent36 BLAT Interface Description & Search Example To In-Silico PCR tool Or upload Enter sequence Limits

37. Copyright OpenHelix. No use or reproduction without express written consent37 Results of BLAT Search Example Alignment Details – check 1st Your sequence Genomic Your sequence Genomic Color-coded New line – “Your Sequence from BLAT Search”

38. Copyright OpenHelix. No use or reproduction without express written consent38 In-Silico PCR – Search Sequences with Primers Specs Flip R-Primer

39. Copyright OpenHelix. No use or reproduction without express written consent39 In-Silico PCR Results Linked genomic location, product size & primer sequences, respectively T m for primers, conditions, link to Primer3 Predicted Product

40. Copyright OpenHelix. No use or reproduction without express written consent40 UCSC Archaeal Genome Browser Agenda UCSC Archaeal Genome Browser: http://archaea.ucsc.edu/ Introduction & Credits Basic Browsing & Searching Species-Specific Gateway Display Advanced Techniques Sequence Searching Summary Exercises

41. Help & Info Copyright OpenHelix. No use or reproduction without express written consent41 A User-Friendly Interface Many easy ways to begin exploring 1 2 3 http://archaea.ucsc.edu/ More than 50 species 4

42. Copyright OpenHelix. No use or reproduction without express written consent42 A Powerful Genome Browser Link to even more details Scroll, zoom, search, jump, configure, and more!

43. Copyright OpenHelix. No use or reproduction without express written consent43 Many Handy Tools & Options - Easy to Access

44. Copyright OpenHelix. No use or reproduction without express written consent44 UCSC Archaeal Genome Browser Agenda UCSC Archaeal Genome Browser: http://archaea.ucsc.edu/ Introduction & Credits Basic Browsing & Searching Species-Specific Gateway Display Advanced Techniques Sequence Searching Summary Exercises

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