ArticleNucleic acids research2011
The Gypsy Database (GyDB) of mobile genetic elements: release 2.0.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 217 papers.
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217 citing papers in PubMed.
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- A comprehensive annotation of conserved protein domains in human endogenous retroviruses.NAR genomics and bioinformatics · 2026Article
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- Complete mitochondrial sequencing reveals the horizontal transfer and gene rearrangement ofFrontiers in plant science · 2026Article
- Dynamic evolution of retroviral envelope-derived sequences in primates.Virus evolution · 2026Article
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- Discovery and Evolutionary Analysis of a Novel Genus of Endogenous Pararetroviruses with Long Terminal Repeats.Genome biology and evolution · 2025Article
- High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae.Genome research · 2025Article
- CREATE: a novel attention-based framework for efficient classification of transposable elements.Briefings in bioinformatics · 2025Article
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157 more citing papers are in PubMed but not listed here.
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15 authors.
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Abstract
This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org.
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