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

James J. Campanella, Ledion Bitincka, John Smalley

Research output: Contribution to journalArticle

591 Citations (Scopus)

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.

Original languageEnglish
Article number29
JournalBMC Bioinformatics
Volume4
DOIs
StatePublished - 10 Jul 2003

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Unit matrix
DNA sequences
Protein Sequence
DNA Sequence
Alignment
Software
Categorization
Proteins
Sequence Alignment
Computer Applications
Research Personnel
Windows operating system
Operating Systems
Open Source
Computer applications
Pairwise
DNA
Genes
Gene
Calculate

Keywords

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

Cite this

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MatGAT : An application that generates similarity/identity matrices using protein or DNA sequences. / Campanella, James J.; Bitincka, Ledion; Smalley, John.

In: BMC Bioinformatics, Vol. 4, 29, 10.07.2003.

Research output: Contribution to journalArticle

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T2 - An application that generates similarity/identity matrices using protein or DNA sequences

AU - Campanella, James J.

AU - Bitincka, Ledion

AU - Smalley, John

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