COMBAT - Combined DNA/protein alignment

The program combat implements the method for combined DNA/protein alignment described in:

Comparison of coding DNA. Christian N. S. Pedersen, Rune B. Lyngsø and Jotun Hein. In Proceedings of the 9th Annual Symposium on Combinatorial Pattern Matching (CPM), July 1998.

A set of slides that describes the combined DNA/protein alignment method implemented by combat, and compares it to other alignment methods, was presented at the Algorithmique et Biologie seminar on "Annotation - Concepts and Methods", Pasteur Institute, December 14-16, 1999.

WWW Interface

A WWW interface for online usage of combat has been developed by Christian Stenz using <bigwig>. Unfortunately the interface is based on software which is no longer maintained and is therefore currently unavailable, but another WWW interface to combat has been made available by Catherine Letondal, Institute Pasteur, as part of an impressive collection of software for biology.

Local Installation and usage

The implementation of combat is mainly done by Tejs Scharling. The implementation is done in C. To install combat download combat-1.0.tar.gz, unpack it (tar xzf combat-1.0.tar.gz), and type make in the subdirectory combat-1.0.

The alignment program is used as

combat controlfile

where controlfile is the name of a file that describes the two sequences to align and the distance matrices and gap-cost functions to use. The format of the controlfile is described in the README file distributed together with the source code.