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.
Composition Alignment Simulation allows one to align thousands of random sequences with different parameters and analyze results graphically to figure statistically meaningful scores. Because this is experimental, it is now restricted to collaborators only.