Exer 5 - Skeleton - Spring, 2001

Exercise 5 - BIMM 141 - Spring 2001

{Answer the Questions at the end as you proceed through the Exercise}

{A. TIGR - The Institute for Genomic Research}

{1. Peruse the TIGR site to see what is there and get a feel for what TIGR does}

{2. TIGR Microbial Database: Completed Genomes}

{3. TIGR Microbial Database: Incomplete Genomes}

{4. Other TIGR Databases}

{5. TIGR Gene Indices}

{6. TIGR Software Tools}

{B. NCBI Genomic Resources}

{1. Entrez Genomes}

{2. NCBI Microbial Genomes}

{3. Examine the "Graphical view" and "Coding regions" of a region of the chosen Genome}

{4. NCBI Specific Organism Resources}

{C. Specific Organism Resources}

{1. NCBI Yeast Genome Site}

{2. Stanford Saccharomyces Genome Database - SGD}

{3. Munich Information center for Protein Sequences- MIPS - for Yeast}

{4. NCBI Fly Genome Site}

{5. Examine Features of a Fly Chromosome using the Map View Graphics}

{6. Select a Fly Gene and Examine Information Available}

{Click on "LocusID" for your Fly Gene}

{7. Examine your Fly Gene in FlyBase}

{Find the link to "The Interactive Fly" and examine this site}

{8. Examine your Fly Gene in GadFly at BDGP}

{Try using the "GeneSeen" Map Viewer}

{D. Information on a Human Gene}

{1. Find a Human Gene to work with ... Gene Ontology terms}

{2. NCBI Resources available for your Human Gene}

{3. GeneCard for your Human Gene}

{4. Ensembl Resources available for your Human Gene}

{a. Search Ensembl for your Gene using the keyword previously used}

{b. View your Gene at Ensembl}

{5. UCSC Resources available for your Human Gene}

{a. Search UCSC for your Gene using the keyword previously used}

{b. View your Gene at UCSC}

{c. Direct links between Ensembl and UCSC}

{E. Questions}

1. What is the mission of TIGR?

2. Who is Chairman of the Board of Trustees of TIGR?

3. From the TIGR "What's New" page, what is Anopheles gambiae and why is its sequence interesting?

4. What are the three Microbial "Domains" at TIGR?

5. What is the size range of genomes present in the TIGR complete microbial genome list?

6. What is the TIGR Comprehensive Microbial Resource (CMR)?

7. Briefly describe three main features of the TIGR Genome Browser.

8. Why is the TIGR Genome Browser NOT used with organisms whose genomes are incompletely sequenced?

9. Comment on five of the Eukaryotes whose genomes are currently being sequenced.

10. What is the purpose of the TIGR Gene Indices?

11. What is TIGR EGAD?

12. What are "software tools"?

13. What is the general focus of the TIGR Software Tools?

14. For the Microbial Genomes, what is the TaxPlot? the TaxTable? the ProtTable?

15. What is the purpose of the Microbial Genome "List of projects" web page?

16. What are three DNA entities that are shown in the NCBI Genome "Graphical View"?

17. How does the "Graphical View" differ in its presentation from that of the "Coding Region"?

18. How does the NCBI "Prominant Organisms" Genome Web page differ from the NCBI "All Organisms" Web page?

19. Comment on similarities and differences between the NCBI Organism Web sites for Arabidopsis, C. elegans, D. melanogaster, and S. cerevisiae.

20. What are the primary types of information present on an NCBI Organism Chromosome page, such as that for your chosen Yeast Chromosome?

21. What is the NCBI RefSeq project? What is its purpose? What is the Accession Format that is used?

22. At SGD, briefly describe the links to "Sequence Analysis and Tools", "Maps", and "Sacch3D".

23. At MIPS, briefly describe the links to "Chromosome Display", "Pathways", and "Functional Analysis Projects".

24. What is the single most annoying feature of the MIPS Web site?

25. What are the four levels of detail for Entrez Map Viewer? Briefly describe each.

26. What organisms are currently represented in the Entrez Map Viewer?

27. What are the primary options and features present in the NCBI Map View graphics display for a Fly Chromosome?

28. What do some of the 2-letter symbols to the right in the Entrez Map Viewer stand for?

29. What is LocusLink and its function? What organisms are currently in LocusLink.

30. What is FlyBase and where is it located?

31. What is "The Interactive Fly"?

32. What is GadFly?

33. Briefly describe the layout of the NCBI "Human Genome" Home Page.

34. What is the Gene Ontology (GO) Consortium, and what is its purpose?

35. What are the types of information LocusLink returns for the Loci found in response to your keyword search? What are the one-letter links shown?

36. What does "Variation" mean?

37. What is OMIM, and what information not in LocusLink does it provide about your gene?

38. What is NCBI UniGene, and what information not in LocusLink does it provide about your gene?

39. What is HomoloGene, and what information is present here that is not in LocusLink?

40. What is GeneCard, and where is it?

41. How does the GeneCard information compare with the NCBI information about your gene?

42. How does the Gene information at Ensembl compare with that at NCBI LocusLink?

43. What is the Ensembl "Disease Browser", and how is it related to NCBI?

44. How does the UCSC Graphic Viewer compare with the NCBI MapView and the EBI ContigView ?

45. If you use the direct links between Ensembl and UCSC, do you get the same graphic views as when you find the gene independently at each of the Web sites? If not, what is the difference?

46. What is RepeatMasker and what is it used for?