Sandra Porter has two posts up on how to use Blast to search for a particular protein sequence and to identify unknown proteins. In the first one, she walks through what Blast is (it's always good to review); the BLOSUM 62 scoring matrix that evaluates how well residues align; and finally, as an example, she searches for "Elvis" in a protein sequence. In the second post, Porter goes into more detail on scoring and talks about E values, which are used to normalize results. "If an E value is low, say below 0.01, then the match is significant. If the E value is higher, the match might still be significant, especially if you have a short sequence," she writes.
On the Search for Elvis
Mar 26, 2009