AI Article Synopsis
- Transposable elements (TEs) in eukaryotes can insert into each other, leading to a mix of full-length elements and fragments, complicating their reconstruction and study.
- A new software tool called TE-greedy-nester was developed using a greedy recursive algorithm to improve the recovery of fragmented full-length LTR retrotransposons in genomic data, showing higher accuracy than existing tools.
- The software is available for use at a specified online location and supplementary data can be found in Bioinformatics online.
Article Abstract
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.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7755421 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btaa632 | DOI Listing |
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