ArticleNAR genomics and bioinformatics2022
Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families.
Article in NAR genomics and bioinformatics, 2022. 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.
- Hide and seek: de novo identification in sugar beet reveals impact of non-autonomous LTR retrotransposons.Mobile DNA · 2026Article
- Further varieties of ancient endogenous retrovirus in human DNA.Mobile DNA · 2025Article
- HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation.Nature communications · 2024Article
- The good, the bad and the ugly of transposable elements annotation tools.Genetics and molecular biology · 2024Article
- Recent Advances in Antibiotic-Free Markers; Novel Technologies to Enhance Safe Human Food Production in the World.Molecular biotechnology · 2023Review
- An immune-suppressing protein in human endogenous retroviruses.Bioinformatics advances · 2023Article
- Insights from analyses of low complexity regions with canonical methods for protein sequence comparison.Briefings in bioinformatics · 2022Article
- A beginner's guide to manual curation of transposable elements.Mobile DNA · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The construction of a high-quality multiple sequence alignment (MSA) from copies of a transposable element (TE) is a critical step in the characterization of a new TE family. Most studies of MSA accuracy have been conducted on protein or RNA sequence families, where structural features and strong signals of selection may assist with alignment. Less attention has been given to the quality of sequence alignments involving neutrally evolving DNA sequences such as those resulting from TE replication. Transposable element sequences are challenging to align due to their wide divergence ranges, fragmentation, and predominantly-neutral mutation patterns. To gain insight into the effects of these properties on MSA accuracy, we developed a simulator of TE sequence evolution, and used it to generate a benchmark with which we evaluated the MSA predictions produced by several popular aligners, along with Refiner, a method we developed in the context of our RepeatModeler software. We find that MAFFT and Refiner generally outperform other aligners for low to medium divergence simulated sequences, while Refiner is uniquely effective when tasked with aligning high-divergent and fragmented instances of a family.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.