NTRFinder: a software tool to find nested tandem repeats

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 ha...

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Detalles Bibliográficos
Autores principales: Matroud, Atheer A., Hendy, M. D., Tuffley, C. P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Methods Online
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3273788/
https://www.ncbi.nlm.nih.gov/pubmed/22121222
http://dx.doi.org/10.1093/nar/gkr1070
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author Matroud, Atheer A.
Hendy, M. D.
Tuffley, C. P.
author_facet Matroud, Atheer A.
Hendy, M. D.
Tuffley, C. P.
author_sort Matroud, Atheer A.
collection PubMed
description 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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spelling pubmed-32737882012-02-07 NTRFinder: a software tool to find nested tandem repeats Matroud, Atheer A. Hendy, M. D. Tuffley, C. P. Nucleic Acids Res Methods Online 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/. Oxford University Press 2012-02 2011-11-25 /pmc/articles/PMC3273788/ /pubmed/22121222 http://dx.doi.org/10.1093/nar/gkr1070 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methods Online
Matroud, Atheer A.
Hendy, M. D.
Tuffley, C. P.
NTRFinder: a software tool to find nested tandem repeats
title NTRFinder: a software tool to find nested tandem repeats
title_full NTRFinder: a software tool to find nested tandem repeats
title_fullStr NTRFinder: a software tool to find nested tandem repeats
title_full_unstemmed NTRFinder: a software tool to find nested tandem repeats
title_short NTRFinder: a software tool to find nested tandem repeats
title_sort ntrfinder: a software tool to find nested tandem repeats
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3273788/
https://www.ncbi.nlm.nih.gov/pubmed/22121222
http://dx.doi.org/10.1093/nar/gkr1070
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