ArticleGene2009
Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences.
Article in Gene, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed.
- A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.Genome biology · 2026Article
- Diversity and genome engineering applications of R2 non-LTR retrotransposons.RNA (New York, N.Y.) · 2026Review
- Long-Standing Activity with Characteristic Genomic Insertion Signatures in Reptilian Bov-B LINEs and Associated Sauria SINEs.Biology · 2026Article
- A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.bioRxiv : the preprint server for biology · 2026Article
- EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis.BMC genomics · 2026Article
- Rewriting the genome: harnessing R2 retrotransposons for precise DNA insertion.Frontiers in genome editing · 2026Review
- Single specimen genome assembly of Culicoides stellifer shows evidence of a non-retroviral endogenous viral element.BMC genomics · 2025Article
- Article
- Transposable elements in Rosaceae: insights into genome evolution, expression dynamics, and syntenic gene regulation.Horticulture research · 2024Article
- Conserved and divergent DNA recognition specificities and functions of R2 retrotransposon N-terminal domains.Cell reports · 2024Article
- The good, the bad and the ugly of transposable elements annotation tools.Genetics and molecular biology · 2024Article
- Human Endogenous Retrovirus-K (HML-2)-Related Genetic Variation: Human Genome Diversity and Disease.Genes · 2023Review
- Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution.BMC biology · 2023Article
- Paleozoic Protein Fossils Illuminate the Evolution of Vertebrate Genomes and Transposable Elements.Molecular biology and evolution · 2022Article
- Maelstrom functions in the production of Siwi-piRISC capable of regulating transposons iniScience · 2022Article
- Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus.Mobile DNA · 2022Article
- Horizontal Transposon Transfer and Its Implications for the Ancestral Ecology of Hydrophiine Snakes.Genes · 2022Article
- Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution.Mobile DNA · 2021Article
- The function of twister ribozyme variants in non-LTR retrotransposition in Schistosoma mansoni.Nucleic acids research · 2021Article
- Retrotransposable Elements: DNA Fingerprinting and the Assessment of Genetic Diversity.Methods in molecular biology (Clifton, N.J.) · 2021Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Rapidly growing number of sequenced genomes requires fast and accurate computational tools for analysis of different transposable elements (TEs). In this paper we focus on a rapid and reliable procedure for classification of autonomous non-LTR retrotransposons based on alignment and clustering of their reverse transcriptase (RT) domains. Typically, the RT domain protein sequences encoded by different non-LTR retrotransposons are similar to each other in terms of significant BLASTP E-values. Therefore, they can be easily detected by the routine BLASTP searches of genomic DNA sequences coding for proteins similar to the RT domains of known non-LTR retrotransposons. However, detailed classification of non-LTR retrotransposons, i.e. their assignment to specific clades, is a slow and complex procedure that is not formalized or integrated as a standard set of computational methods and data. Here we describe a tool (RTclass1) designed for the fast and accurate automated assignment of novel non-LTR retrotransposons to known or novel clades using phylogenetic analysis of the RT domain protein sequences. RTclass1 classifies a particular non-LTR retrotransposon based on its RT domain in less than 10 min on a standard desktop computer and achieves 99.5% accuracy. RT1class1 works either as a stand-alone program installed locally or as a web-server that can be accessed distantly by uploading sequence data through the internet (http://www.girinst.org/RTphylogeny/RTclass1).
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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.