From CAGT

Composition Alignment Overview

Composition Alignment or, more whimsically, scrambled alignment, employs the mechanisms of string matching and string comparison yet avoids the overdependence of those methods on position-by-position matching. In composition alignment, we extend the matching concept to composition matching. Two strings have a composition match if their lengths are equal and they have the same nucleotide content.

• Use Code Download page to get to our compositional alignment library written in C. It also comes with code to compile a console application that utilizes that code.

• Our Web Interface provides an easy way to try out some of the compositional alignment algorithms online.