Methodology article

Poly: a quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA

Jeff W Bizzaro^1,2 and Kenneth A Marx²

¹Bioinformatics Organization, Inc., 28 Pope Street, Hudson, MA 01749 USA

²Center for Intelligent Biomaterials, Dept. of Chemistry, University of Massachusetts Lowell, One University Ave., Lowell, MA 01854 USA

author email corresponding author email

BMC Bioinformatics 2003, 4:22doi:10.1186/1471-2105-4-22

Published:	5 June 2003

Abstract

Background

Simple sequence repeats (SSRs), microsatellites or polymeric sequences are common in DNA and are important biologically. From mononucleotide to trinucleotide repeats and beyond, they can be found in long (> 6 repeating units) tracts and may be characterized by quantifying the frequencies in which they are found and their tract lengths. However, most of the existing computer programs that find SSR tracts do not include these methods.

Results

A computer program named Poly has been written not only to find SSR tracts but to analyze the results quantitatively.

Conclusions

Poly is significant in its use of non-standard, quantitative methods of analysis. And, with its flexible object model and data structure, Poly and its generated data can be used for even more sophisticated analyses.