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

BMC Bioinformatics. 2003 Jul 10;4:29. doi: 10.1186/1471-2105-4-29. Epub 2003 Jul 10.


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.

MeSH terms

  • Animals
  • Computational Biology / methods
  • Computational Biology / trends
  • Computer Graphics / trends
  • Databases, Nucleic Acid / trends
  • Humans
  • Internet
  • Sequence Alignment / trends
  • Sequence Analysis, DNA / methods*
  • Sequence Analysis, Protein / methods*
  • Sequence Homology, Amino Acid*
  • Sequence Homology, Nucleic Acid*
  • Software / trends*