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

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.

Figure 1

Frequency plots (one per panel) for equivalent organism sequence data across a range of GC compositions: Dictyostelium discoideum (0.97 Mb at 26.% GC), Oryza sativa japonica (1.5 Mb at 45.% GC) and Chlamydomonas reinhardtii (0.35 Mb at 62.% GC), including a sequence produced by a random number generator with equal weights between bases (1.0 Mb at 50.% GC). The sequences are concatenated from GenBank document "source" sequences and analyzed by Poly as described in the text. These data are presented solely to illustrate the methods described here and not to describe new research.

Figure 2

Operation of the Poly algorithm on DNA sequences. Panel A illustrates the process for a window size of n = 1. Panel B illustrates the process for n = 3. The dotted lines show which bases are compared. White boxes represent bases which are part of an SSR tract, and black boxes represent those which are not.