Multiple genome sequences alignment algorithm based on coding regions
by Che-Lun Hung, Chun-Yuan Lin, Shih-Cheng Chang, Yeh-Ching Chung, Shu Ju Hsieh, Chuan Yi Tang, Yaw-Ling Lin
International Journal of Computational Biology and Drug Design (IJCBDD), Vol. 4, No. 2, 2011

Abstract: Multiple Sequence Alignment (MSA) is the computational biology tool for facilitating the study of DNA homology, phylogeny determinations and conserved motifs. Many MSA methods have been presented to align protein, DNA, and RNA sequences successfully but not for coding region sequences. Therefore, we propose a heuristic alignment method, CORAL-M, for multiple genome sequences, especially for coding regions. CORAL-M adopts a codon-based probabilistic filtration model and the local optimal alignment solution to align multiple genome sequences in linear time. The experimental results presents that CORAL-M can find more potential function sites than that of other commonly used tools by aligning Enterovirus strains.

Online publication date: Sat, 24-Jan-2015

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