Paper Info
Title
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.
Year
DOI
Venue
1999
10.1093/nar/27.13.2682
NUCLEIC ACIDS RESEARCH
Keywords
Field
DocType
multiple sequence alignment,proteins,sequence alignment,algorithms
Friedman test,Sequence alignment,Alignment-free sequence analysis,Biology,Algorithm,Software,Test case,Local algorithm,Bioinformatics,Genetics,Multiple sequence alignment,Computation
Journal
Volume
Issue
ISSN
27
13
0305-1048
Citations 
PageRank 
References 
202
19.06
4
Authors
3
Search Limit
100202
Name
Order
Citations
PageRank
J D Thompson1803195.00
F Plewniak246647.48
O Poch371670.43