ACLAME: A CLAssification of Mobile genetic Elements, update 2010

By Raphaël Leplae, Gipsi Lima-Mendez, Ariane Toussaint. Nucleic Acids Res., 2009

312 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology

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Citations in the corpus

PHROG: families of prokaryotic virus proteins clustered using remote homology (2021, background): “Presence of proteins annotated unambiguously in the ACLAME database (23) were also retrieved.”
The human gut virome: inter-individual variation and dynamic response to diet. (2011, methodology): “) to an ACLAME prophage sequence, the contigs that were assigned exclusively to the Firmicutes accounted for fully 41% of the total (n This suggests that the prevalence of temperate bacteriophage in the gut may differ among bacterial phyla, though the conclusions depend on representation of phage se”
Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens. (2011, unknown): “Nonetheless, means of directly accessing the mobile gene pool need to be developed, and frameworks for consistent classification and nomenclature of mobile elements need to be used (Roberts et al., 2008a; Leplae et al., 2010).”
Phamerator: a bioinformatic tool for comparative bacteriophage genomics (2011, background): “Because of its computational intensity, it is less well suited to mapping global genome-scale relationships among large phage genome sets, but other programs have been described for this purpose [34,35].”