NTRFINDER: A Software Tool to Find Nested Tandem Repeats

Details NTRFINDER: A Software Tool to Find Nested Tandem Repeats NTRFINDER: A Software Tool to Find Nested Tandem Repeats

2010-06-09

arxiv.org/abs/1006.1730v2

Biology

Quantitative Biology

Quantitative Methods

Scientific paper

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/.

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