NTRFINDER: A Software Tool to Find Nested Tandem Repeats

TL;DR

NTRFinder is a software tool designed to identify nested tandem repeats in DNA sequences, which can serve as phylogenetic markers, aiding in evolutionary and population studies.

Contribution

The paper introduces NTRFinder, a novel algorithm for detecting complex nested tandem repeats in DNA, with applications in phylogenetics and crop history analysis.

Findings

Successfully tested on real and simulated data

Identified nested tandem repeats in taro DNA

Potential use in understanding crop cultivation history

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/.