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.

Základní údaje

Originální název

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

Autoři

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

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 6.937

Kód RIV

RIV/00216224:14330/20:00118965

Organizační jednotka

Fakulta informatiky

DOI

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

UT WoS

000605690100003

EID Scopus

2-s2.0-85098877885

Klíčová slova anglicky

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

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 14. 5. 2021 07:00, RNDr. Pavel Šmerk, Ph.D.

Anotace

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.

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; Pavel JEDLICKA; Ivan VANÁT; Michal ČERVEŇANSKÝ a Eduard KEJNOVSKÝ. TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting. Bioinformatics. OXFORD: OXFORD UNIV PRESS, 2020, roč. 36, č. 20, s. 4991-4999. ISSN 1367-4803. Dostupné z: 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 a Eduard KEJNOVSKÝ. TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting. \textit{Bioinformatics}. OXFORD: OXFORD UNIV PRESS, 2020, roč.~36, č.~20, s.~4991-4999. ISSN~1367-4803. Dostupné z: https://dx.doi.org/10.1093/bioinformatics/btaa632.

Přehled o publikaci