ACLAME: a CLAssification of Mobile genetic Elements, update 2010

• Published in: Nucleic acids research Vol. 38; no. Database issue; pp. D57 - D61
• Main Authors: Leplae, Raphaël, Lima-Mendez, Gipsi, Toussaint, Ariane
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01-01-2010
• Subjects: Algorithms; Bacteriophages - genetics; Computational Biology - methods; Computational Biology - trends; Databases, Genetic; Databases, Nucleic Acid; Genome, Bacterial; Information Storage and Retrieval - methods; Internet; Interspersed Repetitive Sequences; Plasmids - genetics; Repetitive Sequences, Nucleic Acid; Software
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkp938

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.