CORAL-M: Heuristic COding Region ALignment Method for multiple genome sequences

Che Lun Hung, Chun Yuan Lin*, Shih Cheng Chang, Yeh Ching Chung, Shu Ju Hsieh, Chuan Yi Tang, Yaw Ling Lin

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

2 Scopus citations

Abstract

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.

Original languageEnglish
Title of host publication2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010
Pages223-228
Number of pages6
DOIs
StatePublished - 2010
Event2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010 - HongKong, China
Duration: 18 12 201021 12 2010

Publication series

Name2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010

Conference

Conference2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010
Country/TerritoryChina
CityHongKong
Period18/12/1021/12/10

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