dot matrix analysis

Use one of the sites discussed in the presentation of general Bioinformatics web sites to locate two homologous protein sequences. You may use any of the search methods offered at the site. Your goal is to find two proteins of similar, but NOT IDENTICAL, sequences. Do not start this process with a sequence you found elsewhere; find both at the same site.

2. Copy these two sequences to your PC and save each as a text file. Edit each sequence file so that each is in FASTA-format.

3. Become familiar with the Dotlet web site. If you find another site or downloadable program for making dot plots you are welcome to use it instead.

4. Analyze the pairwise alignment between the two sequences with the Dot Matrix method. Vary the Dot Matrix parameters to investigate where the two sequences are similar. Use two or three different sets of parameters (e.g., window size, threshold, or matrix, but others are possible).

5. Prepare a report to contain the following:

A description of the steps you used to find the two protein sequences and the reasoning behind your choices. You may include printouts of web pages to illustrate what you did. There should be enough information so that I would be able to repeat your steps and get the same results.

A listing of the two FASTA-format protein sequence files you prepared. A discussion of your results. This should include printouts of the Dot Matrix plots, a discussion of which

parameters you used and why, and conclusions about which sections of the sequences are similar. You may find that the printouts of dot plots don't look exactly like what you see on the screen, so you will need to experiment to produce good-looking printed plots.