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NTRFinder: a software tool to find nested tandem repeats
Atheer A Matroud1, M D Hendy, C P Tuffley
1Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand. a.a.matroud@massey.ac.nz
Abstract:
We introduce the software tool NTRFinder to search for a 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 NTRs can be used as phylogenetic and population markers. We have tested our algorithm on both real and simulated data, and present some real NTRs of interest. NTRFinder can be downloaded from http://www.maths.otago.ac.nz/~aamatroud/.
