edited by Roderic Guigó

A Course on Sequence Analysis. Practical

Domain Database Searches

by Roderic Guigó 5/6/97

In this practical we will run a sequence against PFAM, a database by Ewan Birney, of protein domains. In order to characterize the function of an unknow protein, searches against databases of motifs corresponding to protein families may be more sensitive than simple sequence searches. PFAM is a database of protein domains represented as Hidden Markov Models.

WWW DB Tools

We will use:

Step 1. Extract an hypothetical protein from the database

Step 2. Compare the sequence of the hypothetical protein with Pfam domain database