BSCI 380; Comparative Bioinformatics Lab

Homework for the week of October 30, 2006.

A major challenge in bioinformatics is being familiar with the many different databases that are available. You will need to be able to choose the correct database for a problem, and know enough about the database to be able to navigate it comfortably. There are a large number of potentially useful databases, so while you should make an effort to remain up to date on the most important of these resources (e.g., NCBI, SwissProt, JGI, etc.), you will also need to develop the skills to quickly locate and learn to use databases that are appropriate to the problem at hand.

There isn't necessarily a single best solution to this problem. One useful resource is the database of bioinformatics databases (a meta-database) at the University of Pittsburgh library:

http://www.hsls.pitt.edu/guides/genetics/obrc

We will use this resource to explore bioinformatics databases.

1) For your convenience, the databases are organized into 13 categories. These categories are necessarily somewhat arbitrary. Identify at least three pairs of these categories that overlap, explain why you perceive them as overlaping, and for each pairidentify at least one database that could reasonably be categorized in both places.

2) An important area of current research is conserved, non-coding regions of genomes. If you compared two genomes and found a conserved, non-coding region of the genome, which resource(s) would help you determine if this sequence had a structure that had previously been described? What techniques were used to find the data in those databases? What information about the sequence would you need to have to find information in that dataabase?

3) Suppose that you are hired as a bioinformatics expert by a lab that studies the role of inheritance in Alzheimer's disease. Is there a database specific to Alzheimer's disease (hint: yes)? Where did you find it in the Pitt resource? What added advantages does this database have over simply doing a search on PubMed or SCI?

4) What do you think are the five most interesting databases? Give a rank-ordered list, with #1 being the most interesting, and for each explain why you think it is a particularly interesting database.

 

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