ACLAME: A CLAssification of mobile genetic elements
ACLAME: A CLAssification of mobile genetic elements
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DOI：
10.1093/nar/gkh084
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发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Toussaint, A
中科院分区：
文献类型：
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作者：
Leplae, R;Hebrant, A;Toussaint, A
ACLAME数据库（http：aclame-ulb.ac.be）是来自各种来源的原核移动的遗传元件（MGE）的集合和分类，包括所有已知的噬菌体基因组、质粒和转座子。除了提供完整基因组和遗传实体的信息外，它还有助于在蛋白质，基因和更高水平上建立MGE功能模块的全面分类。第一个版本包含来自119个DNA噬菌体的5069种蛋白质的全面分类，分为400多个功能家族。该分类是使用TRIBE-MCL自动生成的，TRIBE-MCL是一种基于图论的马尔可夫聚类算法，使用序列度量作为输入，然后手动策划。通过使用Psi-Blast和隐马尔可夫模型进行额外的序列相似性搜索，通过查阅公共数据库中可用的注释来辅助人工策展。该数据库向公众开放，并向愿意参与其管理的专家志愿者开放。其网页界面允许浏览和查询分类。主要目标是收集和组织在一个合理的方式固有的复杂性MGE，扩展和改善目前与MGE相关的不充分的注释和筛选已知的基因组的验证和发现新的MGE。
The ACLAME database (http://aclame-ulb.ac.be) is a collection and classification of prokaryotic mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to providing information on the full genomes and genetic entities, it alms to build a comprehensive classification of the functional modules of MGEs at the protein, gene and higher levels. This first version contains a comprehensive classification of 5069 proteins from 119 DNA bacteriophages into over 400 functional families. This classification was produced automatically using TRIBE-MCL, a graph-theory-based Markov clustering algorithm that uses sequence measures as input, and then manually curated. Manual curation was aided by consulting annotations available in public databases retrieved through additional sequence similarity searches using Psi-Blast and Hidden Markov Models. The database is publicly accessible and open to expert volunteers willing to participate in its curation. Its web interface allows browsing as well as querying the classification. The main objectives are to collect and organize in a rational way the complexity inherent to MGEs, to extend and improve the inadequate annotation currently associated with MGEs and to screen known genomes for the validation and discovery of new MGEs.