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

BMC Bioinformatics

John Smalley¹  Ledion Bitincka¹  James J Campanella¹ 

[1]Montclair State University, Department of Biology and Molecular Biology, 1 Normal Avenue, Montclair, New Jersey 07043 USA

关键词: similarity matrix;    pairwise analysis;    alignment;    sequence;    protein;    nucleic acid;   

Others  :  1171882
DOI  :  10.1186/1471-2105-4-29

 received in 2003-05-09, accepted in 2003-07-10,  发布年份 2003

【 摘 要 】

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.

【 授权许可】

   
2003 Campanella et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.

【 图 表 】

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