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Mat. Biolog. Bioinform., 2012, Volume 7, Issue 2, Pages 476–492 (Mi mbb117)  

This article is cited in 2 scientific papers (total in 2 papers)

Bioinformatics

Search for Extended Repeats in Genomes Based on the Spectral-Analytical Method

Anton Pankratovab, Maxim Pyatkova, Ruslan Tetueva, Nafisa Nazipovaa, Florents F. Dedusb

a Institite of Mathematical Problems of Biology of the Russian Academy of Sciences
b Moscow State University

Abstract: The spectral-analytical approach to identify diverged extended repeats in genomic sequences presented. The method is based on the multi-scaled integral estimation of the similarity of nucleotide sequences in the space of coefficients of expansion of the curves of GC-and GA-content using classical orthogonal bases. Conditions are found for the optimal approximation, providing automatic detection of different types of repeats (direct and inverted and tandem) for the spectral matrix of similarity. The method works equally well on different scales of data. It can detect fragments of segmental duplications, megasatellite blocks in the genome,as well the regions of synteny. It can be used for a detailed study of chromosome fragments (search for diverged fragments with a moderate length of the repeat unit).

Key words: comparison of genomes, the approximation, the matrix of similarity, pattern recognition, megasatellites, interspersed repeats.

Full text: PDF file (481 kB)
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UDC: 519
Received 15.07.2012, Published 08.08.2012

Citation: Anton Pankratov, Maxim Pyatkov, Ruslan Tetuev, Nafisa Nazipova, Florents F. Dedus, “Search for Extended Repeats in Genomes Based on the Spectral-Analytical Method”, Mat. Biolog. Bioinform., 7:2 (2012), 476–492

Citation in format AMSBIB
\Bibitem{PanPyaTet12}
\by Anton~Pankratov, Maxim~Pyatkov, Ruslan~Tetuev, Nafisa~Nazipova, Florents~F.~Dedus
\paper Search for Extended Repeats in Genomes Based on the Spectral-Analytical Method
\jour Mat. Biolog. Bioinform.
\yr 2012
\vol 7
\issue 2
\pages 476--492
\mathnet{http://mi.mathnet.ru/mbb117}


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    Citing articles on Google Scholar: Russian citations, English citations
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    This publication is cited in the following articles:
    1. A. N. Pankratov, R. K. Tetuev, M. I. Pyatkov, V. P. Toigildin, N. N. Popova, “Spektralno-analiticheskii metod raspoznavaniya netochnykh povtorov v simvolnykh posledovatelnostyakh”, Trudy ISP RAN, 27:6 (2015), 335–344  mathnet  crossref  elib
    2. R. K. Tetuev, M. I. Pyatkov, A. N. Pankratov, “Parallelnyi algoritm globalnogo vyravnivaniya protyazhennykh aminokislotnykh i nukleotidnykh posledovatelnostei”, Matem. biologiya i bioinform., 12:1 (2017), 137–150  mathnet  crossref
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