title: MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences.
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.
authors.affiliation: Montclair State University, Department of Biology and Molecular Biology, 1 Normal Avenue, Montclair, New Jersey 07043 USA. james.campanella@montclair.edu
authors.forename: James J
authors.initials: JJ
authors.lastname: Campanella
authors.forename: Ledion
authors.initials: L
authors.lastname: Bitincka
authors.forename: John
authors.initials: J
authors.lastname: Smalley
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods / Q000639:trends; D003196:Computer Graphics / Q000639:trends; D030561:Databases, Nucleic Acid / Q000639:trends; D006801:Humans; D020407:Internet; D016415:Sequence Alignment / Q000639:trends; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D012984:Software / Q000639:trends*