Strategies for multiple sequence alignment.
We present an overview of multiple sequence alignments to outline the practical consequences for the choices among different techniques and parameters. We begin with a discussion of the scoring methods for quantifying the quality of a multiple sequence alignment, followed by a discussion of the algorithms implemented within a variety of multiple sequence alignment programs. We also discuss additional alignment details such as gap penalty and distance metrics. The paper concludes with a discussion on how to improve alignment quality and the limitations of the techniques described in this paper
Nicholas
Hugh B
HB
Pittsburgh Supercomputing Center, Carnegie Mellon University, PA 15213, USA. nicholas@psc.edu
Ropelewski
Alexander J
AJ
Deerfield
David W
DW
D000465:Algorithms; D019143:Evolution, Molecular; D008957:Models, Genetic; D016415:Sequence Alignment / Q000379:methods*; D012984:Software