ArticleBioinformatics (Oxford, England)2020
TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 18 citations in OpenAlex.
- Sexy ways: approaches to studying plant sex chromosomes.Journal of experimental botany · 2024Review
- Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats.Mobile DNA · 2024Article
- Repetitive DNA sequence detection and its role in the human genome.Communications biology · 2023Review
- Chromosome-scale assemblies ofFrontiers in plant science · 2023Article
- Automatic curation of LTR retrotransposon libraries from plant genomes through machine learning.Journal of integrative bioinformatics · 2022Article
- The clove (Syzygium aromaticum) genome provides insights into the eugenol biosynthesis pathway.Communications biology · 2022Article
- Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes.Frontiers in plant science · 2022Article
- Rapid Genome Evolution and Adaptation ofFrontiers in plant science · 2021Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationTransposable 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.
resultsWe 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. AVAILABILITY AND IMPLEMENTATION: http://gitlab.fi.muni.cz/lexa/nested. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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