NTRFINDER: A Software Tool to Find Nested Tandem Repeats

Abstract

We introduce the software tool NTRFinder to find the complex repetitive structure in DNA we call a nested tandem repeat (NTR). An NTR is a recurrence of two or more distinct tandem motifs interspersed with each other. We propose that nested tandem repeats can be used as phylogenetic and population markers. We have tested our algorithm on both real and simulated data, and present some real nested tandem repeats of interest. We discuss how the NTR found in the ribosomal DNA of taro (Colocasia esculenta) may assist in determining the cultivation prehistory of this ancient staple food crop. NTRFinder can be downloaded from http://www.maths.otago.ac.nz/? aamatroud/.