title: Strategies for multiple sequence alignment.
abstract: 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
authors.affiliation: Pittsburgh Supercomputing Center, Carnegie Mellon University, PA 15213, USA. nicholas@psc.edu
authors.forename: Hugh B
authors.initials: HB
authors.lastname: Nicholas
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Ropelewski
authors.forename: David W
authors.initials: DW
authors.lastname: Deerfield
mesh_terms: D000465:Algorithms; D019143:Evolution, Molecular; D008957:Models, Genetic; D016415:Sequence Alignment / Q000379:methods*; D012984:Software