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. 2012 Feb;40(3):e17.
doi: 10.1093/nar/gkr1070. Epub 2011 Nov 25.

NTRFinder: a software tool to find nested tandem repeats

Atheer A Matroud  1 , M D Hendy, C P Tuffley
Affiliations

NTRFinder: a software tool to find nested tandem repeats

Atheer A Matroud et al. Nucleic Acids Res. 2012 Feb.

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/.

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Figures

Figure 1.
Figure 1.
Flowchart of the NTRFinder algorithm.
Figure 2.
Figure 2.
Percentage of NTRs found in the synthetic sequences.
Figure 3.
Figure 3.
Running time of NTRFinder (on a Pentium Dual core T4300 2.1 GHz) plotted against segment length on a log–log scale. The search was performed on segments of different lengths, with the minimum and maximum TR lengths set to 8 and 50, respectively. The distribution suggests the running time is approximately linear with the sequence length.
See this image and copyright information in PMC

References

    1. Weitzmann MN, Woodford KJ, Usdin K. DNA Secondary Structures and the Evolution of Hypervariable Tandem Arrays. J. Biol. Chem. 1997;272:9517–9523. - PubMed
    1. Wells RD. Molecular basis of genetic instability of triplet repeats. J. Biol. Chem. 1996;271:2875–2878. - PubMed
    1. Macdonald ME, Ambrose CM, Duyao MP, Myers RH, Lin C, Srinidhi L, Barnes G, Taylor SA, James M, Groot N. A novel gene containing a trinucleotide repeat that is expanded and unstable on huntington's disease chromosomes. the huntington's disease collaborative research group. Cell. 1993;72:971–983. - PubMed
    1. Fu YH, Pizzuti A, Jr, Fenwick RG, King J, Rajnarayan S, Dunne PW, Dubel J, Nasser GA, Ashizawa T, de Jong P, et al. An unstable triplet repeat in a gene related to myotonic muscular dystrophy. Science. 1992;255:1256–1258. - PubMed
    1. Hauth AM, Joseph DA. Beyond tandem repeats: complex pattern structures and distant regions of similarity. Bioinformatics. 2002;18(Suppl. 1):S31–S37. - PubMed

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