The gypsy database (GyDB) of mobile genetic elements: release 2.0

Carlos Llorens , Ricardo Futami , Laura Covelli , Laura Dominguez-Escriba , Jose M. Viu , Daniel Tamarit (1) , Jose Aguilar-Rodriguez (1) , Miguel Vicente-Ripolles (2) , Gonzalo Fuster , Guillermo P. Bernet (3) , Florian Maumus (4) , Alfonso Munoz-Pomer (2) , Jose M. Sempere (2) , Amparo Latorre (5) , Andrès Moya (5)

1 UV - Universitat de València
2 UPV - Universitat Politècnica de València = Universitad Politecnica de Valencia = Polytechnic University of Valencia
3 IVIA - Instituto Valenciano de Investigaciones Agrarias - Institut Valencià d'Investigacions Agraries - Valencian Institute for agricultural Research
4 URGI - Unité de Recherche Génomique Info
5 CIBERESP - Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública = Consortium for Biomedical Research of Epidemiology and Public Health

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.

Mots clés: retroelements; phylogeny; software; terminal repeat sequences; databases genetic

Domaines: Sciences du Vivant [q-bio]; Biologie végétale

Carlos Llorens, Ricardo Futami, Laura Covelli, Laura Dominguez-Escriba, Jose M. Viu, et al.. The gypsy database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Research, 2011, 39 (S1), pp.D70-D74. ⟨10.1093/nar/gkq1061⟩. ⟨hal-02648997⟩