Evolution of multiple alignments

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Genomics and proteomics technologies have led to aparadigm shift in bioinformatics, where thetraditional reductionist approach is replaced by amore global, integrated view. In this context, multiple sequence alignments provide an idealenvironment for the reliable integration ofinformation from a complete genome to a gene and itsrelated products. In this work, the sequence analysisfield is reviewed and three example developments aredescribed: (i) a benchmark for the objectiveevaluation of multiple alignment algorithms, (ii) amultiple alignment ontology (MAO) for nucleic acid orprotein sequences and structures, (iii) aninformation management system (MACSIMS) that exploitsthe multiple alignment and the organisation providedby the ontology. The work is central tobioinformatics today and should be particularlyuseful to researchers working in various fields, suchas genome analysis, target characterisation forstructural proteomics, the study of human geneticpathologies, or the development of new drug discoverystrategies.