title: Multiple genome sequences alignment algorithm based on coding regions.
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.
authors.affiliation: Department of Computer Science and Communication Engineering, Providence University, Taichung 43301, Taiwan. clhung@pu.edu.tw
authors.forename: Che-Lun
authors.initials: CL
authors.lastname: Hung
authors.forename: Chun-Yuan
authors.initials: CY
authors.lastname: Lin
authors.forename: Shih-Cheng
authors.initials: SC
authors.lastname: Chang
authors.forename: Yeh-Ching
authors.initials: YC
authors.lastname: Chung
authors.forename: Shu Ju
authors.initials: SJ
authors.lastname: Hsieh
authors.forename: Chuan Yi
authors.initials: CY
authors.lastname: Tang
authors.forename: Yaw-Ling
authors.initials: YL
authors.lastname: Lin
mesh_terms: D000465:Algorithms; D000818:Animals; D003627:Data Interpretation, Statistical; D004770:Enterovirus / Q000145:classification / Q000235:genetics; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D009154:Mutation; D016415:Sequence Alignment / Q000706:statistics & numerical data*; D049490:Systems Biology / Q000706:statistics & numerical data