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

Result code in 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>
Alternative codes found
RIV/68081707:_____/20:00539921
Result on the web
<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>

Result language
angličtina
Original language name
TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting
Original language description
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.
Czech name
—
Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project
<a href="/en/project/GA18-00258S" target="_blank" >GA18-00258S: The role of transposable elements in the dynamics of plant genomes</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2020
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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