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The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

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The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

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dc.contributor.author Llorens, Carlos es_ES
dc.contributor.author Futami, Ricardo es_ES
dc.contributor.author Covelli, Laura es_ES
dc.contributor.author Domínguez-Escriba, Laura es_ES
dc.contributor.author Viu, Jose M. es_ES
dc.contributor.author Tamarit, Daniel es_ES
dc.contributor.author Aguilar-Rodríguez, Jose es_ES
dc.contributor.author Vicente Ripollés, Miguel es_ES
dc.contributor.author Fuster, Gonzalo es_ES
dc.contributor.author Bernet, Guillermo P es_ES
dc.contributor.author Maumus, Florian es_ES
dc.contributor.author Munoz-Pomer, Alfonso es_ES
dc.contributor.author Sempere Luna, José María es_ES
dc.contributor.author Latorre, Amparo es_ES
dc.contributor.author Moya, Andres es_ES
dc.date.accessioned 2013-04-29T10:18:06Z
dc.date.available 2013-04-29T10:18:06Z
dc.date.issued 2011
dc.identifier.issn 0305-1048
dc.identifier.uri http://hdl.handle.net/10251/28298
dc.description.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. © The Author(s) 2010. Published by Oxford University Press. es_ES
dc.description.sponsorship Centro de Desarrollo Tecnologico Industrial (CDTI) (grant IDI-20100007, partial); Empresa Nacional de Innovacion, S.A (ENISA) (17092008, partial); IMPIVA (IMIDTA/2009/118 and IMDTA/2010/740, partial); European Regional Development Fund (ERDF); Ministerio de Ciencia e Innovacion (MICINN) (Torres-Quevedo grants PTQ-09-01-00020, PTQ-09-01-00670 and PTQ-10-03552, partial). Funding for open access charge: University of Valencia. en_EN
dc.language Inglés es_ES
dc.publisher Oxford University Press (OUP): Policy C - Option B es_ES
dc.relation.ispartof Nucleic Acids Research es_ES
dc.rights Reconocimiento - No comercial (by-nc) es_ES
dc.subject Virus protein es_ES
dc.subject Article es_ES
dc.subject Caulimoviridae es_ES
dc.subject Chemistry es_ES
dc.subject Classification es_ES
dc.subject Computer program es_ES
dc.subject Genetic database es_ES
dc.subject Genetics es_ES
dc.subject Long terminal repeat es_ES
dc.subject Phylogeny es_ES
dc.subject Retroposon es_ES
dc.subject Retrovirus es_ES
dc.subject Access to information es_ES
dc.subject Cauliflower mosaic virus es_ES
dc.subject Data analysis software es_ES
dc.subject DNA structure es_ES
dc.subject Eukaryote evolution es_ES
dc.subject Genetic line es_ES
dc.subject Genetic variability es_ES
dc.subject Hidden Markov model es_ES
dc.subject Mobile genetic element es_ES
dc.subject Nonhuman es_ES
dc.subject Phylogenetic tree es_ES
dc.subject Priority journal es_ES
dc.subject Protein domain es_ES
dc.subject Sequence analysis es_ES
dc.subject Transposon es_ES
dc.subject Databases, Genetic es_ES
dc.subject Retroelements es_ES
dc.subject Retroviridae es_ES
dc.subject Retroviridae Proteins es_ES
dc.subject Software es_ES
dc.subject Terminal Repeat Sequences es_ES
dc.subject.classification LENGUAJES Y SISTEMAS INFORMATICOS es_ES
dc.title The Gypsy Database (GyDB) of mobile genetic elements: release 2.0 es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1093/nar/gkq1061
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//IDI-20100007/ES/PROYECTO GYPSY DATABASE: LA BASE DE DATOS COLABORATIVA DE ELEMENTOS GENÉTICOS MÓVILES/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/ENISA//17092008/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/Generalitat Valenciana//IMIDTA%2F2009%2F118/ES/Gypsy Database Project And Biotechvana Bioinformatics Ii/ / es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//PTQ-09-01-00020/ES/PTQ-09-01-00020/ / es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//PTQ-09-01-00670/ES/PTQ-09-01-00670/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/Generalitat Valenciana//IMDTA%2F2010%2F740/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MICINN//PTQ-10-03552/ES/PTQ-10-03552/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Sistemas Informáticos y Computación - Departament de Sistemes Informàtics i Computació es_ES
dc.description.bibliographicCitation Llorens, C.; Futami, R.; Covelli, L.; Domínguez-Escriba, L.; Viu, JM.; Tamarit, D.; Aguilar-Rodríguez, J.... (2011). The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Research. 39:70-74. https://doi.org/10.1093/nar/gkq1061 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion http://nar.oxfordjournals.org/content/39/suppl_1/D70.abstract es_ES
dc.description.upvformatpinicio 70 es_ES
dc.description.upvformatpfin 74 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 39 es_ES
dc.relation.senia 210862
dc.identifier.pmid 21036865 en_EN
dc.identifier.pmcid PMC3013669 en_EN
dc.contributor.funder Ministerio de Ciencia e Innovación es_ES
dc.contributor.funder Empresa Nacional de Innovacion, S.A. es_ES
dc.contributor.funder Universitat de València
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