Identifying multiple alignment regions satisfying simple formulas and patterns.

Abstract

When studying multiple alignments of genomic sequences one frequently aims to locate and count regions which satisfy a set of constraints. These regions may be putatively functional, but researchers may also be interested in quantifying the frequency of occurrences of certain patterns. We have developed a program that applies simple formulas and pattern specifications to multiple alignments, reporting the positions and counts of conforming regions. As an example, we have navigated a 15-species alignment of the CAV2-CAV1 region and outlined some findings regarding PPARgamma binding sites. Our software and the accompanying documentation can be obtained at no charge by contacting the authors. It can also be accessed at http://ranger.uta.edu/~nick/compgen