Bioinformatics assignment

The purpose of this assignment is to become familiar with various biological databases and to understand the type of information and tools that each database contains. You will also reinforce learning about genetic causes of disease.

Go to the National Center for Biotechnology Information (NCBI) website.

http://www.ncbi.nlm.nih.gov/

 NB if you’d like to view tutorials on how to use or navigate some elements of this website, you can find them here: http://www.ncbi.nlm.nih.gov/education/tutorials/

Assignment:

1. Identify a disease or trait for which at least one specific gene has been linked (you can start out in the OMIM database or PubMed to identify a disease or gene, drop down menu next to search bar on NCBI homepage)
2. Give a brief overview (one paragraph) of the trait or disease (can be cut and pasted).
3. How is this disease typically treated (if at all)?
4. Give the DNA or RNA sequence of one gene that is relevant to this trait or disease. (If it’s a long sequence, just give the accession number, which probably begins with NM) (Can find this information as follows: When you’re within the OMIM gene page, go to DNA on right hand menu, choose NCBI RefSeq)
5. Give the amino acid sequence of this gene. (single letter code, on same page as 4)
6. On what chromosome is this gene located?
7. Is the gene involved in any other known traits?
8. Is the normal function of this gene/protein known? What does it do?
9. What are the titles of 3 important journal articles on this disease?
10. Has the 3-dimensional structure of the protein encoded by this gene been determined? (see the protein data bank: http://www.rcsb.org/pdb/home/home.do)
11. Are there any clinical trials currently being conducted on this disease (go to www.clinicaltrials.gov)? Briefly, describe a couple of clinical trials.
12. Find another gene (using Blast-can link from the gene sequence page) that shares some homology with your gene http://blast.be-md.ncbi.nlm.nih.gov/Blast.cgi
13. Visit the gene ontology page (http://www.geneontology.org/). Does this website provide any additional information?
14. How much of the above information can you find using Google, Wikipedia, Wolfram Alpha, or other favorite search engines and sites? Are there other databases or websites that may have relevant information?
15. What suggestions would you make (change certain prompts, make it more open ended, walk through a tutorial as a class, etc) to enhance your learning from this assignment?

If you’re having trouble finding a disease with an obvious genetic defect to work on, try one of the following:

Huntington’s Disease, Hemophilia, Sickle Cell Anemia, Narcolepsy, Long QT Syndrome, Lactose Intolerance, Muscular Dystrophy, Color blindness, Beta-thalassemia, von Hippel Lindau syndrome, Cystic Fibrosis