title: Codon-based encoding for DNA sequence analysis.
abstract: With the exponential growth of biological sequence data (DNA or Protein Sequence), DNA sequence analysis has become an essential task for biologist to understand the features, functions, structures, and evolution of species. Encoding DNA sequences is an effective method to extract the features from DNA sequences. It is commonly used for visualizing DNA sequences and analyzing similarities/dissimilarities between different species or cells. Although there have been many encoding approaches proposed for DNA sequence analysis, we require more elegant approaches for higher accuracy. In this paper, we propose a noble encoding approach for measuring the degree of similarity/dissimilarity between different species. Our approach can preserve the physiochemical properties, positional information, and the codon usage bias of nucleotides. An extensive performance study shows that our approach provides higher accuracy than existing approaches in terms of the degree of similarity.
authors: Department of Computer Engineering, Kyung Hee University, 1-Seocheon-dong, Yongin-si 446-701, Gyeonggi-do, Republic of Korea.
authors: Byeong-Soo
authors: BS
authors: Jeong
authors: Department of Computer Engineering, Kyung Hee University, 1-Seocheon-dong, Yongin-si 446-701, Gyeonggi-do, Republic of Korea.
authors: A T M
authors: AT
authors: Golam Bari
authors: Department of Computer Engineering, Kyung Hee University, 1-Seocheon-dong, Yongin-si 446-701, Gyeonggi-do, Republic of Korea.
authors: Mst
authors: M
authors: Rokeya Reaz
authors: Department of Computer Engineering, Kyung Hee University, 1-Seocheon-dong, Yongin-si 446-701, Gyeonggi-do, Republic of Korea.
authors: Seokhee
authors: S
authors: Jeon
authors: Department of Computer Engineering, Kyung Hee University, 1-Seocheon-dong, Yongin-si 446-701, Gyeonggi-do, Republic of Korea.
authors: Chae-Gyun
authors: CG
authors: Lim
authors: Department of Computer Science, Korean Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea. Electronic address: hojinc@kaist.ac.kr.
authors: Ho-Jin
authors: HJ
authors: Choi
mesh_terms: D003062:Codon; D004252:DNA Mutational Analysis; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D003062:Codon
keywords: Codon; DNA visulization; Encoding DNA sequence; Sequence similarity