Bioinformatique des Génomes et des Réseaux, Université Libre de Bruxelles, Boulevard du Triomphe, 1050 Bruxelles, Belgium.
Nucleic Acids Res. 2010 Jan;38(Database issue):D57-61. doi: 10.1093/nar/gkp938. Epub 2009 Nov 23.
The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). In addition to providing information on the MGEs content, classifications are available at various levels of organization. At the gene/protein level, families group similar sequences that are expected to share the same function. Families of four or more proteins are manually assigned with a functional annotation using the GeneOntology and the locally developed ontology MeGO dedicated to MGEs. At the genome level, evolutionary cohesive modules group sets of protein families shared among MGEs. At the population level, networks display the reticulate evolutionary relationships among MGEs. To increase the coverage of the phage sequence space, ACLAME version 0.4 incorporates 760 high-quality predicted prophages selected from the Prophinder database. Most of the data can be downloaded from the freely accessible ACLAME web site (http://aclame.ulb.ac.be). The BLAST interface for querying the database has been extended and numerous tools for in-depth analysis of the results have been added.
ACLAME 数据库致力于收集、分析和分类已测序的移动遗传元件（MGEs，特别是噬菌体和质粒）。除了提供有关 MGEs 内容的信息外，还可以在各种组织层次上提供分类。在基因/蛋白质水平上，家族将相似的序列分组，这些序列预计具有相同的功能。具有四个或更多蛋白质的家族使用 GeneOntology 和专门用于 MGEs 的本地开发的 MeGO 本体论手动分配功能注释。在基因组水平上，进化凝聚模块将 MGEs 之间共享的蛋白质家族集分组。在种群水平上，网络显示 MGEs 之间的网状进化关系。为了增加噬菌体序列空间的覆盖范围，ACLAME 版本 0.4 纳入了从 Prophinder 数据库中选择的 760 个高质量预测的噬菌体。大多数数据可从免费访问的 ACLAME 网站（http://aclame.ulb.ac.be）下载。用于查询数据库的 BLAST 接口已得到扩展，并添加了许多用于深入分析结果的工具。
