Multiple sequence alignment: algorithms and applications

Abstract

Elucidation of interrelationships among sequence, structure, function, and evolution (FESS relationships) of a family of genes or gene products is a central theme of modern molecular biology. Multiple sequence alignment has been proven to be a powerful tool for many fields of studies such as phylogenetic reconstruction, illumination of functionally important regions, and prediction of higher order structures of proteins and RNAs. However, it is far too trivial to automatically construct a multiple alignment from a set of related sequences. A variety of methods for solving this computationally difficult problem are reviewed. Several important applications of multiple alignment for elucidation of the FESS relationships are also discussed. For a long period, progressive methods have been the only practical means to solve a multiple alignment problem of appreciable size. This situation is now changing with the development of new techniques including several classes of iterative methods. Today's progress in multiple sequence alignment methods has been made by the multidisciplinary endeavors of mathematicians, computer scientists, and biologists in various fields including biophysicists in particular. The ideas are also originated from various backgrounds, pure algorithmics, statistics, thermodynamics, and others. The outcomes are now enjoyed by researchers in many fields of biological sciences. In the near future, generalized multiple alignment may play a central role in studies of FESS relationships. The organized mixture of knowledge from multiple fields will ferment to develop fruitful results which would be hard to obtain within each area. I hope this review provides a useful information resource for future development of theory and practice in this rapidly expanding area of bioinformatics.