TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting Article Swipe
Matej Lexa
,
Pavel Jedlička
,
Ivan Vanat
,
Michal Červeňanský
,
Eduard Kejnovský
·
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btaa632
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1093/bioinformatics/btaa632
Motivation 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. Results 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. Availability and implementation http://gitlab.fi.muni.cz/lexa/nested. Supplementary information Supplementary data are available at Bioinformatics online.
Related Topics
Concepts
Repressor lexA
Retrotransposon
Transposable element
Computer science
Software
Nesting (process)
Genome
Greedy algorithm
Biology
Algorithm
Computational biology
Genetics
Programming language
Gene
Repressor
Metallurgy
Materials science
Transcription factor
Metadata
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- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/bioinformatics/btaa632
- https://academic.oup.com/bioinformatics/article-pdf/36/20/4991/35065244/btaa632.pdf
- OA Status
- hybrid
- Cited By
- 18
- References
- 51
- Related Works
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- OpenAlex ID
- https://openalex.org/W3043090500
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3043090500Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/bioinformatics/btaa632Digital Object Identifier
- Title
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TE-greedy-nester: structure-based detection of LTR retrotransposons and their nestingWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2020Year of publication
- Publication date
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2020-07-07Full publication date if available
- Authors
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Matej Lexa, Pavel Jedlička, Ivan Vanat, Michal Červeňanský, Eduard KejnovskýList of authors in order
- Landing page
-
https://doi.org/10.1093/bioinformatics/btaa632Publisher landing page
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https://academic.oup.com/bioinformatics/article-pdf/36/20/4991/35065244/btaa632.pdfDirect link to full text PDF
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YesWhether a free full text is available
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hybridOpen access status per OpenAlex
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https://academic.oup.com/bioinformatics/article-pdf/36/20/4991/35065244/btaa632.pdfDirect OA link when available
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Repressor lexA, Retrotransposon, Transposable element, Computer science, Software, Nesting (process), Genome, Greedy algorithm, Biology, Algorithm, Computational biology, Genetics, Programming language, Gene, Repressor, Metallurgy, Materials science, Transcription factorTop concepts (fields/topics) attached by OpenAlex
- Cited by
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18Total citation count in OpenAlex
- Citations by year (recent)
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2025: 1, 2024: 4, 2023: 5, 2022: 5, 2021: 3Per-year citation counts (last 5 years)
- References (count)
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51Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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