A New Approach for DNA Sequence Similarity Analysis based on Triplets of Nucleic Acid Bases

A New Approach for DNA Sequence Similarity Analysis based on Triplets of Nucleic Acid Bases

Dan Wei (Cognitive Science Department, Xiamen University, China and Fujian Key Laboratory of the Brain-like Intelligent Systems (Xiamen University), China), Qingshan Jiang (Software School, Xiamen University, China) and Sheng Li (Software School, Xiamen University, China)
DOI: 10.4018/978-1-60960-064-8.ch006
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Abstract

Similarity analysis of DNA sequences is a fundamental research area in Bioinformatics. The characteristic distribution of L-tuple, which is the tuple of length L, reflects the valuable information contained in a biological sequence and thus may be used in DNA sequence similarity analysis. However, similarity analysis based on characteristic distribution of L-tuple is not effective for the comparison of highly conservative sequences. In this paper, a new similarity measurement approach based on Triplets of Nucleic Acid Bases (TNAB) is introduced for DNA sequence similarity analysis. The new approach characterizes both the content feature and position feature of a DNA sequence using the frequency and position of occurrence of TNAB in the sequence. The experimental results show that the approach based on TNAB is effective for analysing DNA sequence similarity.
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Similarity Analysis

The characteristic distribution of L-tuple was studied to extract position feature from DNA sequences by Liu et al. (2007).

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