TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
22 12 2020
22 12 2020
Historique:
received:
11
09
2019
revised:
08
06
2020
accepted:
07
07
2020
pubmed:
15
7
2020
medline:
9
3
2021
entrez:
15
7
2020
Statut:
ppublish
Résumé
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. http://gitlab.fi.muni.cz/lexa/nested. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 32663247
pii: 5871348
doi: 10.1093/bioinformatics/btaa632
pmc: PMC7755421
doi:
Substances chimiques
DNA Transposable Elements
0
Retroelements
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4991-4999Informations de copyright
© The Author(s) 2020. Published by Oxford University Press.
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