Llorens Carlos, Futami Ricardo, Covelli Laura, Domínguez-Escribá Laura, Viu Jose M, Tamarit Daniel, Aguilar-Rodríguez Jose, Vicente-Ripolles Miguel, Fuster Gonzalo, Bernet Guillermo P, Maumus Florian, Munoz-Pomer Alfonso, Sempere Jose M, Latorre Amparo, Moya Andres
Biotechvana, Parc Científic, Universitat de València, Calle Catedrático José Beltrán 2, 46980 Paterna, València, Spain.
Nucleic Acids Res. 2011 Jan;39(Database issue):D70-4. doi: 10.1093/nar/gkq1061. Epub 2010 Oct 29.
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.
本文介绍了移动遗传元件吉普赛数据库的第二次发布版本（GyDB 2.0）：这是一个基于病毒和转座元件的系统发育分类（按谱系和蛋白质结构域）来研究其进化动态的项目。吉普赛数据库（GyDB）是一个持续推进的长期项目，由于移动元件具有高度的分子多样性，需要分几个阶段完成。GyDB 2.0配备了一个维基，以便其他研究人员参与该项目。当前数据库阶段和范围是长末端重复序列（LTR）反转录元件及其相关元件。GyDB 2.0是基于对Ty3/吉普赛、逆转录病毒科、Ty1/科皮亚和Bel/Pao LTR反转录元件以及植物花椰菜花叶病毒科副逆转录病毒的分析而进行的更新。在上述主题方面，此更新增加了以下内容：（i）分布在多个网页上的各种描述和综述；（ii）基于蛋白质的系统发育树，其中系统发育水平被分配给不同分类的元件；（iii）一个多序列比对、谱系特异性隐马尔可夫模型和共有序列的集合，称为GyDB集合；（iv）更新的RefSeq数据库以及BLAST和HMM服务器，以促进对新的LTR反转录元件和花椰菜花叶病毒查询的序列特征分析；以及（v）一个文献服务器。GyDB 2.0可在http://gydb.org上获取。
