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. 2004 Jan 1;32(Database issue):D45-9.
doi: 10.1093/nar/gkh084.

ACLAME: a CLAssification of Mobile genetic Elements

Raphaël Leplae  1 , Aline Hebrant, Shoshana J Wodak, Ariane Toussaint
Affiliations

ACLAME: a CLAssification of Mobile genetic Elements

Raphaël Leplae et al. Nucleic Acids Res. .

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.

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Figures

Figure 1
Figure 1
Three views of the MGE genomes loaded in ACLAME. (a) The list of hosts where the MGE genomes are found. (b) The list of MGE genomes with their major features. (c) The list of proteins found in a MGE genome. Links to external databases are provided in all pages.
Figure 2
Figure 2
Access to the clustered MGE proteins. (a) The list of clusters with the number of proteins found in each of them, the functional annotation and the number of hits found using HMMs in SCOP, NCBI-NRDB and Swiss-Prot. Some tools are provided to further analyze these clusters. (b) Content of a cluster with the list of proteins, their original annotation and the MGE genome where they are found. Access to the database searches with Psi-Blast 3 iterations in Swiss-Prot and/or NCBI-NRDB is also provided.
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