Thompson, J: Evolution of multiple alignments

Genomics and proteomics technologies have led to a paradigm shift in bioinformatics, where the traditional reductionist approach is replaced by a more global, integrated view. In this context, multiple sequence alignments provide an ideal environment for the reliable integration of information from a complete genome to a gene and its related products. In this work, the sequence analysis field is reviewed and three example developments are described: (i) a benchmark for the objective evaluation of multiple alignment algorithms, (ii) a multiple alignment ontology (MAO) for nucleic acid or protein sequences and structures, (iii) an information management system (MACSIMS) that exploits the multiple alignment and the organisation provided by the ontology. The work is central to bioinformatics today and should be particularly useful to researchers working in various fields, such as genome analysis, target characterisation for structural proteomics, the study of human genetic pathologies, or the development of new drug discovery strategies.