Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost

doi:10.1186/1471-2105-7-524

BMC Bioinformatics

Volume 7

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Research article

Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost

Shinsuke Yamada¹^,2 , Osamu Gotoh²^,3 and Hayato Yamana¹

¹Department of Computer Science, Graduate School of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan

²Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-43 Aomi, Koto-ku, Tokyo 135-0064, Japan

³Department of Intelligence Science and Technology, Graduate School of Informatics, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan

author email corresponding author email

BMC Bioinformatics 2006, 7:524doi:10.1186/1471-2105-7-524


Published:	1 December 2006

Abstract

Background

Multiple sequence alignment (MSA) is a useful tool in bioinformatics. Although many MSA algorithms have been developed, there is still room for improvement in accuracy and speed. In the alignment of a family of protein sequences, global MSA algorithms perform better than local ones in many cases, while local ones perform better than global ones when some sequences have long insertions or deletions (indels) relative to others. Many recent leading MSA algorithms have incorporated pairwise alignment information obtained from a mixture of sources into their scoring system to improve accuracy of alignment containing long indels.

Results

We propose a novel group-to-group sequence alignment algorithm that uses a piecewise linear gap cost. We developed a program called PRIME, which employs our proposed algorithm to optimize the well-defined sum-of-pairs score. PRIME stands for Profile-based Randomized Iteration MEthod. We evaluated PRIME and some recent MSA programs using BAliBASE version 3.0 and PREFAB version 4.0 benchmarks. The results of benchmark tests showed that PRIME can construct accurate alignments comparable to the most accurate programs currently available, including L-INS-i of MAFFT, ProbCons, and T-Coffee.

Conclusion

PRIME enables users to construct accurate alignments without having to employ pairwise alignment information. PRIME is available at http://prime.cbrc.jp/ webcite.