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The Gypsy Database (GyDB) of mobile genetic elements: release 2.0.
Nucleic Acids Res. 2011 Jan; 39(Database issue):D70-4.NA

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.

Authors+Show Affiliations

Biotechvana, Parc Científic, Universitat de València, Calle Catedrático José Beltrán 2, 46980 Paterna, València, Spain. carlos.llorens@uv.esNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

21036865

Citation

Llorens, Carlos, et al. "The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0." Nucleic Acids Research, vol. 39, no. Database issue, 2011, pp. D70-4.
Llorens C, Futami R, Covelli L, et al. The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res. 2011;39(Database issue):D70-4.
Llorens, C., Futami, R., Covelli, L., Domínguez-Escribá, L., Viu, J. M., Tamarit, D., Aguilar-Rodríguez, J., Vicente-Ripolles, M., Fuster, G., Bernet, G. P., Maumus, F., Munoz-Pomer, A., Sempere, J. M., Latorre, A., & Moya, A. (2011). The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Research, 39(Database issue), D70-4. https://doi.org/10.1093/nar/gkq1061
Llorens C, et al. The Gypsy Database (GyDB) of Mobile Genetic Elements: Release 2.0. Nucleic Acids Res. 2011;39(Database issue):D70-4. PubMed PMID: 21036865.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. AU - Llorens,Carlos, AU - Futami,Ricardo, AU - Covelli,Laura, AU - Domínguez-Escribá,Laura, AU - Viu,Jose M, AU - Tamarit,Daniel, AU - Aguilar-Rodríguez,Jose, AU - Vicente-Ripolles,Miguel, AU - Fuster,Gonzalo, AU - Bernet,Guillermo P, AU - Maumus,Florian, AU - Munoz-Pomer,Alfonso, AU - Sempere,Jose M, AU - Latorre,Amparo, AU - Moya,Andres, Y1 - 2010/10/29/ PY - 2010/11/2/entrez PY - 2010/11/3/pubmed PY - 2011/4/29/medline SP - D70 EP - 4 JF - Nucleic acids research JO - Nucleic Acids Res VL - 39 IS - Database issue N2 - 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. SN - 1362-4962 UR - https://www.unboundmedicine.com/medline/citation/21036865/The_Gypsy_Database__GyDB__of_mobile_genetic_elements:_release_2_0_ L2 - https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkq1061 DB - PRIME DP - Unbound Medicine ER -