ArticleNucleic acids research2009
MGEScan-non-LTR: computational identification and classification of autonomous non-LTR retrotransposons in eukaryotic genomes.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed.
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- TransposonUltimate: software for transposon classification, annotation and detection.Nucleic acids research · 2022Article
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- Small RNA pathways in the nematode Ascaris in the absence of piRNAs.Nature communications · 2022Article
- Chromosome restructuring and number change during the evolution of Morus notabilis and Morus alba.Horticulture research · 2022Article
- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
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- Transposable elements expression in Rhinella marina (cane toad) specimens submitted to immune and stress challenge.Genetica · 2021Article
- Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus.BMC genomics · 2021Article
- Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution.Mobile DNA · 2021Article
- Genomic anatomy of male-specific microchromosomes in a gynogenetic fish.PLoS genetics · 2021Article
- Distinct Retrotransposon Evolution Profile in the Genome of Rabbit (Oryctolagus cuniculus).Genome biology and evolution · 2021Article
- Transposons-Based Clonal Diversity in Trematode Involves Parts of CR1 (LINE) in Eu- and Heterochromatin.Genes · 2021Article
- Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis).GigaScience · 2021Article
- Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models.Genomics, proteomics & bioinformatics · 2021Article
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2 authors.
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Abstract
Computational methods for genome-wide identification of mobile genetic elements (MGEs) have become increasingly necessary for both genome annotation and evolutionary studies. Non-long terminal repeat (non-LTR) retrotransposons are a class of MGEs that have been found in most eukaryotic genomes, sometimes in extremely high numbers. In this article, we present a computational tool, MGEScan-non-LTR, for the identification of non-LTR retrotransposons in genomic sequences, following a computational approach inspired by a generalized hidden Markov model (GHMM). Three different states represent two different protein domains and inter-domain linker regions encoded in the non-LTR retrotransposons, and their scores are evaluated by using profile hidden Markov models (for protein domains) and Gaussian Bayes classifiers (for linker regions), respectively. In order to classify the non-LTR retrotransposons into one of the 12 previously characterized clades using the same model, we defined separate states for different clades. MGEScan-non-LTR was tested on the genome sequences of four eukaryotic organisms, Drosophila melanogaster, Daphnia pulex, Ciona intestinalis and Strongylocentrotus purpuratus. For the D. melanogaster genome, MGEScan-non-LTR found all known 'full-length' elements and simultaneously classified them into the clades CR1, I, Jockey, LOA and R1. Notably, for the D. pulex genome, in which no non-LTR retrotransposon has been annotated, MGEScan-non-LTR found a significantly larger number of elements than did RepeatMasker, using the current version of the RepBase Update library. We also identified novel elements in the other two genomes, which have only been partially studied for non-LTR retrotransposons.
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