Unit 1: Databases & Queries
Project 1: Basic Local Alignment Search Tool

Note: You will need a copy of the following paper:

Altschul S.F., Gish W., Miller W., Myers E. and Lipman D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215(3): 403-410.

Objectives:

Learn something about BLAST.

• Understand BLAST as a primary software package for bioinformatics.
• Survey applications of BLAST.
• Study the BLAST algorithm as an example of bioinformatics software development.
  

The project consists of class participation, analysis of the BLAST paper, and written answers to the questions below. Points = 10. Due at the end of class on 09/11/2003.

 
Getting started:

The paper selected for this project addresses the problem of finding sequences in a database which are similar to the query sequence, whatever it may be.

The next steps:

1. As you read the paper, make note of any terms or concepts which you do not understand. Create an outline or idea map of the concepts you do understand.

2. In answering the questions below, you may work with others in the class including instructors. The exercises you have done also may provide some of the answers.

Discussion and report summary:

Due on 09/11/2003, are the answers to the following questions:

2. What general function does BLAST perform?

3. List the URLs of some servers that run BLAST through a web or e-mail interface.

4. Where on the web can BLAST program files be obtained (i.e., downloaded for local installation)?

5. The authors of BLAST claim that BLAST is fast, flexible, and capable of estimating statistical properties of the alignments it finds. What evidence do the authors offer in support of these claims?

6. What special features of the BLAST algorithm distinguish it from other approaches to database sequence similarity searching?

7. When BLAST executes a query, what main tasks or steps occupy the computer's time?

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