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

2. TAIR: The Arabidopsis Information Resource A resource for Arabidopsis thaliana genetic and molecular data Materials prepared by: Jennifer Williams, Ph.D. www.openhelix.com Updated: Q3 2010 Version 1

3. Copyright OpenHelix. No use or reproduction without express written consent3 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR: http://www.arabidopsis.orghttp://www.arabidopsis.org

4. TAIR Introduction Copyright OpenHelix. No use or reproduction without express written consent4 TAIR: comprehensive, current information about Arabidopsis thaliana Complete genome sequence, gene structure, metabolism, maps, markers, publications and more Updated regularly http://www.arabidopsis.org

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

6. TAIR Publications Copyright OpenHelix. No use or reproduction without express written consent6 http://nar.oxfordjournals.org/cgi/reprint/36/suppl_1/D1009

7. Many Tools & Options From TAIR Homepage Copyright OpenHelix. No use or reproduction without express written consent7 Stocks - Arabidopsis Biological Resource Center (ABRC) tools Portals - resources and information organized by topic Download - TAIR ftp site for downloading various materials Submit - where you can contribute to TAIR efforts News - several methods of accessing info, including joining newsgroups and posting job ads

8. Many Tools & Options From TAIR Homepage Copyright OpenHelix. No use or reproduction without express written consent8 Search by: Genes, DNA/Clones, Ecotypes, Keywords, GO, History, Markers, Microarray, etc. Textpresso: new text-mining system Tools: GBrowser, Seqviewer, Mapviewer, Metabolic Pathways, Sequence Alignments, and more!

9. TAIR Online Help Copyright OpenHelix. No use or reproduction without express written consent9 Click Help Search Tutorials FAQ Quick Start Tools Glossary curator@arabidopsis.org

10. Copyright OpenHelix. No use or reproduction without express written consent10 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR: http://www.arabidopsis.orghttp://www.arabidopsis.org

11. Searches Copyright OpenHelix. No use or reproduction without express written consent11 http://www.arabidopsis.org keyword Click

12. Search Overview Copyright OpenHelix. No use or reproduction without express written consent12 Click Many specific searches available on the Search Overview page Our example will be the Genes search

13. Gene Search Options Copyright OpenHelix. No use or reproduction without express written consent13 Select

14. More Gene Search Options Copyright OpenHelix. No use or reproduction without express written consent14 Select

15. Restricting Your Gene Search & Output Options Copyright OpenHelix. No use or reproduction without express written consent15 Select

16. Gene Search Example Copyright OpenHelix. No use or reproduction without express written consent16 Select Click

17. Gene Search Results Copyright OpenHelix. No use or reproduction without express written consent17

18. Copyright OpenHelix. No use or reproduction without express written consent18 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR: http://www.arabidopsis.orghttp://www.arabidopsis.org

19. Basic Browsers Copyright OpenHelix. No use or reproduction without express written consent19 http://www.arabidopsis.org Click

20. ABRC Browser Copyright OpenHelix. No use or reproduction without express written consent20 Mutants Transgenic lines Genomic libraries Clones

21. 2010 Projects Copyright OpenHelix. No use or reproduction without express written consent21 Click

22. Monsanto SNP and Ler Collections Copyright OpenHelix. No use or reproduction without express written consent22 Click

23. Gene Families Copyright OpenHelix. No use or reproduction without express written consent23 Click

24. Gene Symbols Copyright OpenHelix. No use or reproduction without express written consent24 Click

25. Ontologies/Keywords Copyright OpenHelix. No use or reproduction without express written consent25 Click Enter terms

26. Archived e-Journals Copyright OpenHelix. No use or reproduction without express written consent26 Click

27. Copyright OpenHelix. No use or reproduction without express written consent27 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR: http://www.arabidopsis.orghttp://www.arabidopsis.org

28. GBrowse Access Copyright OpenHelix. No use or reproduction without express written consent28 Click http://www.arabidopsis.org

29. GBrowse Search Copyright OpenHelix. No use or reproduction without express written consent29 Click

30. GBrowse Overview and Details Copyright OpenHelix. No use or reproduction without express written consent30 Locus Protein cDNAs Transposons Polymorphisms

31. GBrowse VISTA Plots Copyright OpenHelix. No use or reproduction without express written consent31

32. GBrowse Tracks Copyright OpenHelix. No use or reproduction without express written consent32 Click

33. GBrowse Customized Details Copyright OpenHelix. No use or reproduction without express written consent33

34. Copyright OpenHelix. No use or reproduction without express written consent34 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR: http://www.arabidopsis.orghttp://www.arabidopsis.org

35. AraCyc Metabolic Pathway Tool Access Copyright OpenHelix. No use or reproduction without express written consent35 Click http://www.arabidopsis.org

36. AraCyc Metabolic Pathway Tool Homepage Copyright OpenHelix. No use or reproduction without express written consent36 Search Click Intro Browse Submit Release

37. AraCyc Metabolic Pathway Search Copyright OpenHelix. No use or reproduction without express written consent37 Select Click

38. AraCyc Metabolic Pathway Browser Copyright OpenHelix. No use or reproduction without express written consent38 Click

39. AraCyc Metabolic Pathway Browser Options Copyright OpenHelix. No use or reproduction without express written consent39 Click

40. Pathway Information Page-Top Copyright OpenHelix. No use or reproduction without express written consent40

41. Pathway Information Page-Bottom Copyright OpenHelix. No use or reproduction without express written consent41

42. Copyright OpenHelix. No use or reproduction without express written consent42 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR: http://www.arabidopsis.orghttp://www.arabidopsis.org

43. Sequence Alignment Tools Copyright OpenHelix. No use or reproduction without express written consent43 Click http://www.arabidopsis.org

44. BLAST Search Copyright OpenHelix. No use or reproduction without express written consent44 Click Select

45. BLAST Options Copyright OpenHelix. No use or reproduction without express written consent45 Click Select

46. Submitting Your BLAST Search Copyright OpenHelix. No use or reproduction without express written consent46 Insert sequence here Click

47. BLAST Results Copyright OpenHelix. No use or reproduction without express written consent47

48. Copyright OpenHelix. No use or reproduction without express written consent48 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR: http://www.arabidopsis.orghttp://www.arabidopsis.org

49. Additional Tools: Bulk Data Retrieval Copyright OpenHelix. No use or reproduction without express written consent49 Click http://www.arabidopsis.org

50. Bulk Data Retrieval Tool Copyright OpenHelix. No use or reproduction without express written consent50 Click

51. Bulk Data Retrieval Tool: Gene Descriptions Copyright OpenHelix. No use or reproduction without express written consent51 Search Options Output Options

52. Additional Tools Copyright OpenHelix. No use or reproduction without express written consent52 Click http://www.arabidopsis.org

53. Chromosomal Map Tool Copyright OpenHelix. No use or reproduction without express written consent53 Your results

54. Restriction Analysis Tool Copyright OpenHelix. No use or reproduction without express written consent54

55. Restriction Analysis Results-Top Copyright OpenHelix. No use or reproduction without express written consent55 Enzymes used

56. Restriction Analysis Results-Bottom Copyright OpenHelix. No use or reproduction without express written consent56 Key Enzymes that don’t cut

57. Copyright OpenHelix. No use or reproduction without express written consent57 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR: http://www.arabidopsis.orghttp://www.arabidopsis.org

58. Summary Comprehensive data for Arabidopsis thaliana Freely available to the public and updated regularly Copyright OpenHelix. No use or reproduction without express written consent58 http://www.arabidopsis.org

59. Many Topics Easily searchable topics range from molecular biology and biochemistry to classical genetics Copyright OpenHelix. No use or reproduction without express written consent59

60. Copyright OpenHelix. No use or reproduction without express written consent60 TAIR Agenda Introduction and Credits Searches Basic Browsers Genome Browser AraCyc Metabolic Pathway Viewer Sequence Alignment Tools Additional Tools Summary Exercises TAIR: http://www.arabidopsis.orghttp://www.arabidopsis.org

61. Copyright OpenHelix. No use or reproduction without express written consent61