TY - GEN
T1 - CORAL-M
AU - Hung, Che Lun
AU - Lin, Chun Yuan
AU - Chang, Shih Cheng
AU - Chung, Yeh Ching
AU - Hsieh, Shu Ju
AU - Tang, Chuan Yi
AU - Lin, Yaw Ling
PY - 2010
Y1 - 2010
N2 - Multiple sequence alignment is a scientific tool to assist the study of DNA homology, phylogeny determinations, and conserved motifs identification. Various heuristic MSA methods have been presented to obtain the resulting alignment for multiple sequences. Although these alignment tools are able to align protein, DNA, and RNA sequences successfully, they are not such successful in aligning coding region sequences because the resulting alignments maybe not consistent with practical observations. Therefore, we propose a method, CORAL-M, a heuristic coding regions alignment method for multiple genome sequences, especially for coding regions. CORAL-M adopts a probabilistic filtration model and the local optimal solution to align genome sequences (codon to codon with the wobble mask rule) by the sliding windows and, thus, obtains the near-optimal alignment in linear time. In the experimental results, CORAL-M can be used to find the potential function sites by aligning viral strains of Poliovirus 1-3, Enterovirus 71, and Coxsackievirus 16.
AB - Multiple sequence alignment is a scientific tool to assist the study of DNA homology, phylogeny determinations, and conserved motifs identification. Various heuristic MSA methods have been presented to obtain the resulting alignment for multiple sequences. Although these alignment tools are able to align protein, DNA, and RNA sequences successfully, they are not such successful in aligning coding region sequences because the resulting alignments maybe not consistent with practical observations. Therefore, we propose a method, CORAL-M, a heuristic coding regions alignment method for multiple genome sequences, especially for coding regions. CORAL-M adopts a probabilistic filtration model and the local optimal solution to align genome sequences (codon to codon with the wobble mask rule) by the sliding windows and, thus, obtains the near-optimal alignment in linear time. In the experimental results, CORAL-M can be used to find the potential function sites by aligning viral strains of Poliovirus 1-3, Enterovirus 71, and Coxsackievirus 16.
UR - http://www.scopus.com/inward/record.url?scp=79952034584&partnerID=8YFLogxK
U2 - 10.1109/BIBMW.2010.5703803
DO - 10.1109/BIBMW.2010.5703803
M3 - Conference contribution
AN - SCOPUS:79952034584
SN - 9781424483044
T3 - 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010
SP - 223
EP - 228
BT - 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010
Y2 - 18 December 2010 through 21 December 2010
ER -
