ACLAME: a CLAssification of Mobile genetic Elements.

TitleACLAME: a CLAssification of Mobile genetic Elements.
Publication TypeJournal Article
Year of Publication2004
AuthorsLeplae, R., Hebrant A., Wodak S. J., and Toussaint A.
JournalNucleic Acids Res
Volume32
IssueDatabase issue
PaginationD45-9
Date Published2004 Jan 1
ISSN1362-4962
KeywordsBacteriophages, Computational Biology, Databases, Nucleic Acid, Information Storage and Retrieval, Internet, Interspersed Repetitive Sequences, Prokaryotic Cells, Software, User-Computer Interface
Abstract

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 aims 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.

DOI10.1093/nar/gkh084
Alternate JournalNucleic Acids Res.
PubMed ID14681355
PubMed Central IDPMC308818