Local Sequence Similarities

Abstract

Abstract In today’s genomic era, the use of computer-based comparative genetic sequence analysis has become routine. It is used to identify the function of newly sequenced genes, to identify conserved functional sites, to reconstruct probable evolutionary histories, and to investigate many other biological questions. DNA and protein comparative sequence analysis is often considered to be the founding aspect of what is now called Bioinformatics and Genomics. Given that the development of computational tools played a key role, a bit of history will help in understanding both the motivations and the sequence of ideas that led to many comparative sequence tools, including the local dynamic or Smith–Waterman alignment algorithm.