Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost |
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| Authors: | Shinsuke Yamada Osamu Gotoh Hayato Yamana |
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| Institution: | (1) Department of Computer Science, Graduate School of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku Tokyo, 169-8555, Japan;(2) Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-43 Aomi, Koto-ku Tokyo, 135-0064, Japan;(3) Department of Intelligence Science and Technology, Graduate School of Informatics, Kyoto University, Yoshida-Honmachi, Sakyo-ku Kyoto, 606-8501, Japan |
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| 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. |
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