Sonoma State University
CS Colloquium | October 12, 2006

Scoring Alignment Gaps In The Twilight Zone

Barbara Chapman, Sonoma State University

Stevenson Hall 1300
12:00 PM - 12:50 PM

Scoring systems for protein sequence alignment, the main tool for annotating new genes, perform poorly in the most informative comparisons. In this ‘twilight zone’ of amino acid identity, existing scoring methods miss true relationships and cannot consistently reject chance similarities. This talk covers a proposed structure-sensing scoring method that performs well on tests of execution time, sensitivity, and alignment quality.