Detailed Information on Publication Record
2018
TE-nester: a recursive software tool for structure-based discovery of nested transposable elements
LEXA, Matej, Radovan LAPÁR, Pavel JEDLIČKA, Ivan VANÁT, Michal ČERVEŇANSKÝ et. al.Basic information
Original name
TE-nester: a recursive software tool for structure-based discovery of nested transposable elements
Authors
LEXA, Matej (703 Slovakia, guarantor, belonging to the institution), Radovan LAPÁR (703 Slovakia, belonging to the institution), Pavel JEDLIČKA (203 Czech Republic), Ivan VANÁT (703 Slovakia, belonging to the institution), Michal ČERVEŇANSKÝ (703 Slovakia) and Eduard KEJNOVSKÝ (203 Czech Republic)
Edition
Neuveden, Proceedings 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), p. 2776-2778, 3 pp. 2018
Publisher
IEEE
Other information
Language
English
Type of outcome
Stať ve sborníku
Field of Study
10201 Computer sciences, information science, bioinformatics
Country of publisher
United States of America
Confidentiality degree
není předmětem státního či obchodního tajemství
Publication form
electronic version available online
RIV identification code
RIV/00216224:14330/18:00107385
Organization unit
Faculty of Informatics
ISBN
978-1-5386-5488-0
ISSN
UT WoS
000458654000484
Keywords in English
bioinformatics; software; LTR-retrotransposons; sequence analysis; genome evolution
Tags
International impact, Reviewed
Změněno: 3/5/2019 12:59, RNDr. Pavel Šmerk, Ph.D.
Abstract
V originále
ukaryotic genomes are generally rich in repetitive sequences. LTR retrotransposons are the most abundant class of repetitive sequences in plant genomes. They form segments of genomic sequences that accumulate via individual events and bursts of retrotransposition. A limited number of tools exist that can identify fragments of repetitive sequences that likely originate from a longer, originally unfragmented element, using mostly sequence similarity to guide reconstruction of fragmented sequences. Here, we use a slightly different approach based on structural (as opposed to sequence similarity) detection of unfragmented full-length elements, which are then recursively eliminated from the analyzed sequence to repeatedly uncover unfragmented copies hidden underneath more recent insertions. This approach has the potential to detect relatively old and highly fragmented copies. We created a software tool for this kind of analysis called TE-nester and applied it to a number of assembled plant genomes to discover pairs of nested LTR retrotransposons of various age and fragmentation state. TEnester will allow us to test hypotheses about genome evolution, TE life cycle and insertion history. The software, still under improvement, is available for download from a repository at https://gitlab.fi.muni.cz/lexa/nested.
Links
| GA18-00258S, research and development project |
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