A comprehensive comparison of multiple sequence alignment programs

Abstract

In recent years improvements to existing programs and the introduction of new iterative algorithms have changed the state-of-the-art in protein sequence alignment. This paper presents the first systematic study of the most commonly used alignment programs using BAliBASE benchmark alignments as test cases. Even below the 'twilight zone' at 10-20% residue identity, the best programs were capable of correctly aligning on average 47% of the residues. We show that iterative algorithms often offer improved alignment accuracy though at the expense of computation time. A notable exception was the effect of introducing a single divergent sequence into a set of closely related sequences, causing the iteration to diverge away from the best alignment. Global alignment programs generally performed better than local methods, except in the presence of large N/C-terminal extensions and internal insertions. In these cases, a local algorithm was more successful in identifying the most conserved motifs. This study enables us to propose appropriate alignment strategies, depending on the nature of a particular set of sequences. The employment of more than one program based on different alignment techniques should significantly improve the quality of automatic protein sequence alignment methods. The results also indicate guidelines for improvement of alignment algorithms.

Journal

Title: Nucleic Acids Research

Abbreviated Title: Nucleic Acids Research

Publisher: Oxford University Press (OUP)

ISSN (Print): 0305-1048

ISSN (Electronic): 1362-4962

Publication date Created: July 01 1999

Publication date (Print): July 01 1999

Volume: 27

Issue: 13

Pages: 2682-2690

Article

DOI: 10.1093/nar/27.13.2682

PMC ID: 148477

PubMed ID: 10373585

Copyright statement: © 1999

Product

Self URI (article page): https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/27.13.2682