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Improving Sequence Alignment using Class-Specific Score Matrices

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4 Author(s)
Hai Song Xu ; Coll. of Life Sci. & Bioeng., Beijing Univ. of Technol., Beijing ; Wen Ke Ren ; Xiao Hui Liu ; Xiao Qin Li

Sequence alignment has been a most commonly used method in modern biological research. However, sequence alignment in "Twilight Zone" is still a challenging issue. Three protein class-specific matrices are constructed to investigate whether alignment in "Twilight Zone" can be improved by using class-specific matrices and gap penalties. The substitution pattern differences between different protein classes do improve the performances of the three class-specific matrices. Analyzing amino acids substitution pattern based on different matrices also suggests important information for protein sequence design.

Published in:

Bioinformatics and Biomedical Engineering, 2008. ICBBE 2008. The 2nd International Conference on

Date of Conference:

16-18 May 2008