Introducing variable gap penalties into three-sequence alignment for protein sequences

Che Lun Hung*, Chun Yuan Lin, Yeh Ching Chung, Chuan Yi Tang

*此作品的通信作者

研究成果: Conference contribution同行評審

6 引文 斯高帕斯(Scopus)

摘要

The common-use gap penalty strategies, constant penalty and affine gap penalty, have been adopted in the traditional three-sequence alignment algorithm which considers the insertion, deletion and substitution. However, these strategies are not suitable to protein sequence alignments. For the alignment accuracy of protein sequences, the gap penalty is a major determinant. Incorporating protein structure information to vary the gap penalties can lead to more biologically correct alignments. Here, we present an algorithm to find a global and optimal alignment among three protein sequences by using position-specific gap penalties which allow gap penalties to be varied. Thus, residue-dependent information and protein structure information can be applied to the three-sequence alignment. The experimental results show that our algorithm achieves the significant improvement in the accuracy of alignments than the three-sequence alignment algorithm with the affine gap penalty for protein sequences.

原文English
主出版物標題Proceedings - 22nd International Conference on Advanced Information Networking and Applications Workshops/Symposia, AINA 2008
發行者Institute of Electrical and Electronics Engineers Inc.
頁面726-731
頁數6
ISBN(列印)0769530966, 9780769530963
DOIs
出版狀態Published - 2008
事件22nd International Conference on Advanced Information Networking and Applications Workshops/Symposia, AINA 2008 - Gino-wan, Okinawa, Japan
持續時間: 25 3月 200828 3月 2008

出版系列

名字Proceedings - International Conference on Advanced Information Networking and Applications, AINA
ISSN(列印)1550-445X

Conference

Conference22nd International Conference on Advanced Information Networking and Applications Workshops/Symposia, AINA 2008
國家/地區Japan
城市Gino-wan, Okinawa
期間25/03/0828/03/08

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