CSE 590TV: Computational Biology
Homework 2
January 15, 2003

This is intended to be a much shorter assignment than homework 1.

Reading

Read the BLAST tutorial and guide on the NCBI website. The best pieces I have found so far are

Experiment with some nucleotide and protein queries from your prokaryote, BLASTed against the entire nr database.

Due January 22

A question came up in the first lecture about whether E. coli and humans have any proteins in common. For your very own prokaryote from homework 1, find a protein (say A) whose sequence is very similar to some human protein (say B).
  1. Explain the procedure by which you discovered A and B. (This discovery may require some ingenuity. Ideally you would like to BLAST every protein from your prokaryote against the complete database of human proteins, but this probably is too time-consuming. So you may need to investigate some other resources on the web. If you find this very frustrating, don't worry about it too much: just report the best A-B pair you can find.)
  2. Display an optimal alignment of the sequences of proteins A and B. This alignment can be from BLAST if you like.
  3. If you can find the information for this, write a short paragraph describing the functions of proteins A and/or B, trying to highlight any similarities of function. List your sources.

tompa@cs.washington.edu (Last Update: )