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ACLAME: a CLAssification of Mobile genetic Elements, update 2010
Raphaël Leplae1, Gipsi Lima-Mendez, Ariane Toussaint
1Bioinformatique des Génomes et des Réseaux, Université Libre de Bruxelles, Boulevard du Triomphe, 1050 Bruxelles, Belgium. raphael@bigre.ulb.ac.be
Nucleic Acids Research
|November 26, 2009
Summary
The ACLAME database classifies mobile genetic elements (MGEs), including phages and plasmids, offering functional annotations and evolutionary relationship analyses. It enhances phage sequence coverage with new predicted prophages, providing valuable data for researchers.
Area of Science:
- Genomics
- Bioinformatics
- Microbiology
Background:
- Mobile genetic elements (MGEs) like phages and plasmids are crucial in microbial evolution.
- Comprehensive databases are needed for their collection, analysis, and classification.
- Understanding MGEs aids in studying microbial genetics and evolution.
Purpose of the Study:
- To present the ACLAME database (version 0.4) for MGEs analysis.
- To provide functional annotations and evolutionary insights into MGEs.
- To expand the database with new phage data and analysis tools.
Main Methods:
- Collection and classification of sequenced MGEs (phages, plasmids).
- Functional annotation of gene/protein families using GeneOntology and MeGO.
- Genome-level grouping into evolutionary cohesive modules.
- Population-level network analysis of MGE evolutionary relationships.
- Integration of predicted prophages from the Prophinder database.
Main Results:
- ACLAME database provides multi-level classifications for MGEs.
- Functional annotations are available for protein families.
- Evolutionary relationships are visualized at genome and population levels.
- Version 0.4 includes 760 predicted prophages, enhancing phage sequence coverage.
- Extended BLAST interface and new analysis tools are available.
Conclusions:
- ACLAME is a valuable resource for MGEs research, offering comprehensive data and analysis tools.
- The database facilitates functional and evolutionary studies of phages and plasmids.
- Expanded data and tools in version 0.4 improve MGEs sequence space coverage and research capabilities.
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