Search for Highly Divergent SINE repeats in the Rice Genome-Reference-Cited by-同舟云学术

Search for Highly Divergent SINE repeats in the Rice Genome

Published:2020 Issue:4 Volume:36 Page:15-20
ISSN:2500-2341
Container-title:Biotekhnologiya
language:ru
Short-container-title:Biiotehnologiâ (Mosk.)

Author:

Kamionskaya A.M.¹,Korotkov E.V.²

Affiliation:

1. Fundamentals of Biotechnology, Federal Research Centre, Russian Academy of Sciences., Moscow, 119071, Russia

2. Fundamentals of Biotechnology, Federal Research Centre, Russian Academy of Sciences., Moscow, 119071, Russia, 2National Research Nuclear University, Moscow Engineering Physics Institute, Moscow, 115409, Russia

Abstract

In this article, we present a new method for searching for highly divergent copies of SINE elements in a genome. The method is based on the correlation of neighboring symbols both in constructing a positional weight matrix for a sequence of interest and in the genome scanning procedure. This makes possible to increase the alphabet size and, accordingly, the resolution capacity of the method. Using it, we found new copies of SINE repeats in the rice genome that have not been annotated before. The method was tested and compared with the RepeatMasker program; false positives were evaluated. SINE elements, retrotransposons, alignment-based methods, sequence similarity The work was partly supported by the RFBR Grant no. 20-016-00057.

Publisher

National Research Center Kurchatov Institute

Subject

Ecology,Applied Microbiology and Biotechnology,Biotechnology

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