Methodology article

MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences

James J Campanella , Ledion Bitincka and John Smalley

Montclair State University, Department of Biology and Molecular Biology, 1 Normal Avenue, Montclair, New Jersey 07043 USA

author email corresponding author email

BMC Bioinformatics 2003, 4:29doi:10.1186/1471-2105-4-29

Published:	10 July 2003

Abstract

Background

The rapid increase in the amount of protein and DNA sequence information available has become almost overwhelming to researchers. So much information is now accessible that high-quality, functional gene analysis and categorization has become a major goal for many laboratories. To aid in this categorization, there is a need for non-commercial software that is able to both align sequences and also calculate pairwise levels of similarity/identity.

Results

We have developed MatGAT (Matrix Global Alignment Tool), a simple, easy to use computer application that generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data.

Conclusions

The advantages of this program over other software are that it is open-source freeware, can analyze a large number of sequences simultaneously, can visualize both sequence alignment and similarity/identity values concurrently, employs global alignment in calculations, and has been formatted to run under both the Unix and the Microsoft Windows Operating Systems. We are presently completing the Macintosh-based version of the program.