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BMC Bioinformatics. 2003 Jul 10;4:29. Epub 2003 Jul 10.

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

Author information

  • 1Montclair State University, Department of Biology and Molecular Biology, 1 Normal Avenue, Montclair, New Jersey 07043 USA. james.campanella@montclair.edu

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.

PMID:
12854978
[PubMed - indexed for MEDLINE]
PMCID:
PMC166169
Free PMC Article

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