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

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F20%3A00118965" target="_blank" >RIV/00216224:14330/20:00118965 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/68081707:_____/20:00539921

Výsledek na webu

<a href="https://academic.oup.com/bioinformatics/article/36/20/4991/5871348" target="_blank" >https://academic.oup.com/bioinformatics/article/36/20/4991/5871348</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/bioinformatics/btaa632" target="_blank" >10.1093/bioinformatics/btaa632</a>

Jazyk výsledku

angličtina

Název v původním jazyce

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

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

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

Popis výsledku anglicky

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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

<a href="/cs/project/GA18-00258S" target="_blank" >GA18-00258S: Úloha transposonů v dynamice rostlinných genomů</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2020

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Bioinformatics

ISSN

1367-4803

e-ISSN

—

Svazek periodika

36

Číslo periodika v rámci svazku

20

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

9

Strana od-do

4991-4999

Kód UT WoS článku

000605690100003

EID výsledku v databázi Scopus

2-s2.0-85098877885