TE-nester: a recursive software tool for structure-based
discovery of nested transposable elements

D 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.

Základní údaje

Originální název

TE-nester: a recursive software tool for structure-based discovery of nested transposable elements

Autoři

LEXA, Matej (703 Slovensko, garant, domácí), Radovan LAPÁR (703 Slovensko, domácí), Pavel JEDLIČKA (203 Česká republika), Ivan VANÁT (703 Slovensko, domácí), Michal ČERVEŇANSKÝ (703 Slovensko) a Eduard KEJNOVSKÝ (203 Česká republika)

Vydání

Neuveden, Proceedings 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), od s. 2776-2778, 3 s. 2018

Nakladatel

IEEE

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

elektronická verze "online"

Kód RIV

RIV/00216224:14330/18:00107385

Organizační jednotka

Fakulta informatiky

ISBN

978-1-5386-5488-0

ISSN

DOI

http://dx.doi.org/10.1109/BIBM.2018.8621071

UT WoS

000458654000484

Klíčová slova anglicky

bioinformatics; software; LTR-retrotransposons; sequence analysis; genome evolution

Štítky

bioinformatics, software, transposable elements

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 3. 5. 2019 12:59, RNDr. Pavel Šmerk, Ph.D.

Anotace

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.

Návaznosti

GA18-00258S, projekt VaV

Název: Úloha transposonů v dynamice rostlinných genomů (Akronym: TRANSPOSONY_DRG)

Investor: Grantová agentura ČR, Úloha transposonů v dynamice rostlinných genomů

Citovat

LEXA, Matej, Radovan LAPÁR, Pavel JEDLIČKA, Ivan VANÁT, Michal ČERVEŇANSKÝ a Eduard KEJNOVSKÝ. TE-nester: a recursive software tool for structure-based discovery of nested transposable elements. Online. In Zheng Huiru. Proceedings 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). Neuveden: IEEE, 2018, s. 2776-2778. ISBN 978-1-5386-5488-0. Dostupné z: https://dx.doi.org/10.1109/BIBM.2018.8621071.

@inproceedings{1527963,
   author = {Lexa, Matej and Lapár, Radovan and Jedlička, Pavel and Vanát, Ivan and Červeňanský, Michal and Kejnovský, Eduard},
   address = {Neuveden},
   booktitle = {Proceedings 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},
   doi = {http://dx.doi.org/10.1109/BIBM.2018.8621071},
   editor = {Zheng Huiru},
   keywords = {bioinformatics; software; LTR-retrotransposons; sequence analysis; genome evolution},
   howpublished = {elektronická verze "online"},
   language = {eng},
   location = {Neuveden},
   isbn = {978-1-5386-5488-0},
   pages = {2776-2778},
   publisher = {IEEE},
   title = {TE-nester: a recursive software tool for structure-based discovery of nested transposable elements},
   year = {2018}
}

TY  - JOUR
ID  - 1527963
AU  - Lexa, Matej - Lapár, Radovan - Jedlička, Pavel - Vanát, Ivan - Červeňanský, Michal - Kejnovský, Eduard
PY  - 2018
TI  - TE-nester: a recursive software tool for structure-based discovery of nested transposable elements
PB  - IEEE
CY  - Neuveden
SN  - 9781538654880
KW  - bioinformatics
KW  - software
KW  - LTR-retrotransposons
KW  - sequence analysis
KW  - genome evolution
N2  - 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.
ER  -

LEXA, Matej, Radovan LAPÁR, Pavel JEDLIČKA, Ivan VANÁT, Michal ČERVEŇANSKÝ a Eduard KEJNOVSKÝ. TE-nester: a recursive software tool for structure-based discovery of nested transposable elements. Online. In Zheng Huiru. \textit{Proceedings 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)}. Neuveden: IEEE, 2018, s.~2776-2778. ISBN~978-1-5386-5488-0. Dostupné z: https://dx.doi.org/10.1109/BIBM.2018.8621071.

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