TE-greedy-nester: structure-based detection of LTR
retrotransposons and their nesting

J 2020

TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting

LEXA, Matej, Pavel JEDLICKA, Ivan VANÁT, Michal ČERVEŇANSKÝ, Eduard KEJNOVSKÝ et. al.

Basic information

Original name

TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting

Authors

LEXA, Matej (703 Slovakia, guarantor, belonging to the institution), Pavel JEDLICKA (203 Czech Republic), Ivan VANÁT (703 Slovakia, belonging to the institution), Michal ČERVEŇANSKÝ (703 Slovakia, belonging to the institution) and Eduard KEJNOVSKÝ (203 Czech Republic)

Edition

Bioinformatics, OXFORD, OXFORD UNIV PRESS, 2020, 1367-4803

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 6.937

RIV identification code

RIV/00216224:14330/20:00118965

Organization unit

Faculty of Informatics

DOI

http://dx.doi.org/10.1093/bioinformatics/btaa632

UT WoS

000605690100003

Keywords in English

TRANSPOSABLE ELEMENTS; VISUALIZATION; ANNOTATION; IDENTIFICATION; PALEONTOLOGY; PROGRAM; SEARCH; FINDER; TENEST

Abstract

V originále

Transposable elements (TEs) in eukaryotes often get inserted into one another, forming sequences that become a complex mixture of full-length elements and their fragments. The reconstruction of full-length elements and the order in which they have been inserted is important for genome and transposon evolution studies. However, the accumulation of mutations and genome rearrangements over evolutionary time makes this process error-prone and decreases the efficiency of software aiming to recover all nested full-length TEs. We created software that uses a greedy recursive algorithm to mine increasingly fragmented copies of full-length LTR retrotransposons in assembled genomes and other sequence data. The software called TE-greedy-nester considers not only sequence similarity but also the structure of elements. This new tool was tested on a set of natural and synthetic sequences and its accuracy was compared to similar software. We found TE-greedy-nester to be superior in a number of parameters, namely computation time and full-length TE recovery in highly nested regions.

Links

GA18-00258S, research and development project

Name: Úloha transposonů v dynamice rostlinných genomů (Acronym: TRANSPOSONY_DRG)

Investor: Czech Science Foundation

Citovat

LEXA, Matej, Pavel JEDLICKA, Ivan VANÁT, Michal ČERVEŇANSKÝ and Eduard KEJNOVSKÝ. TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting. Bioinformatics. OXFORD: OXFORD UNIV PRESS, 2020, vol. 36, No 20, p. 4991-4999. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btaa632.

@article{1767956,
   author = {Lexa, Matej and Jedlicka, Pavel and Vanát, Ivan and Červeňanský, Michal and Kejnovský, Eduard},
   article_location = {OXFORD},
   article_number = {20},
   doi = {http://dx.doi.org/10.1093/bioinformatics/btaa632},
   keywords = {TRANSPOSABLE ELEMENTS; VISUALIZATION; ANNOTATION; IDENTIFICATION; PALEONTOLOGY; PROGRAM; SEARCH; FINDER; TENEST},
   language = {eng},
   issn = {1367-4803},
   journal = {Bioinformatics},
   title = {TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting},
   url = {https://academic.oup.com/bioinformatics/article/36/20/4991/5871348},
   volume = {36},
   year = {2020}
}

TY  - JOUR
ID  - 1767956
AU  - Lexa, Matej - Jedlicka, Pavel - Vanát, Ivan - Červeňanský, Michal - Kejnovský, Eduard
PY  - 2020
TI  - TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting
JF  - Bioinformatics
VL  - 36
IS  - 20
SP  - 4991-4999
EP  - 4991-4999
PB  - OXFORD UNIV PRESS
SN  - 13674803
KW  - TRANSPOSABLE ELEMENTS
KW  - VISUALIZATION
KW  - ANNOTATION
KW  - IDENTIFICATION
KW  - PALEONTOLOGY
KW  - PROGRAM
KW  - SEARCH
KW  - FINDER
KW  - TENEST
UR  - https://academic.oup.com/bioinformatics/article/36/20/4991/5871348
N2  - Transposable elements (TEs) in eukaryotes often get inserted into one another, forming sequences that become a complex mixture of full-length elements and their fragments. The reconstruction of full-length elements and the order in which they have been inserted is important for genome and transposon evolution studies. However, the accumulation of mutations and genome rearrangements over evolutionary time makes this process error-prone and decreases the efficiency of software aiming to recover all nested full-length TEs. We created software that uses a greedy recursive algorithm to mine increasingly fragmented copies of full-length LTR retrotransposons in assembled genomes and other sequence data. The software called TE-greedy-nester considers not only sequence similarity but also the structure of elements. This new tool was tested on a set of natural and synthetic sequences and its accuracy was compared to similar software. We found TE-greedy-nester to be superior in a number of parameters, namely computation time and full-length TE recovery in highly nested regions.
ER  -

LEXA, Matej, Pavel JEDLICKA, Ivan VANÁT, Michal ČERVEŇANSKÝ and Eduard KEJNOVSKÝ. TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting. \textit{Bioinformatics}. OXFORD: OXFORD UNIV PRESS, 2020, vol.~36, No~20, p.~4991-4999. ISSN~1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btaa632.

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