CHAPTER 14

EVOLUTION OF THE CLUSTAL FAMILY OF MULTIPLE SEQUENCE ALIGNMENT PROGRAMS

Mohamed Radhouene Aniba and Julie Thompson

14.1 INTRODUCTION

One of the cornerstones of modern bioinformatics is the comparison or alignment of protein sequences. Multiple alignments are used to compare a set of sequences, either to estimate their overall similarity or to identify locally conserved motifs. As such, classical string-matching algorithms have been applied to the problem as well as many other algorithms, such as dynamic programming, hidden Markov Models, genetic algorithms, and so on. Nevertheless, it is important to keep in mind that the sequences analyzed in biology represent biological molecules (DNA, RNA, or protein) having unique three-dimensional (3-D) structures and specific functions. They act in complex networks, interacting with other molecules in a stable or transitory way within a changing cellular environment.

By placing the sequence in the framework of the overall family, multiple alignments not only identify important structural or functional motifs that have been conserved during evolution but also can highlight particular nonconserved features resulting from specific events or perturbations [32, 15]. As a consequence, multiple sequence comparison or alignment has become a fundamental tool in many different domains in modern molecular biology, from evolutionary studies to prediction of two-dimensional (2-D) of 3-D structure, molecular function, intermolecular interactions, ...

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