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

James J. Campanella, Ledion Bitincka, John Smalley

Research output: Contribution to journalArticlepeer-review

747 Scopus citations


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.

Original languageEnglish
Article number29
JournalBMC Bioinformatics
StatePublished - 10 Jul 2003


  • Alignment
  • Nucleic acid
  • Pairwise analysis
  • Protein
  • Sequence
  • Similarity matrix


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