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Information Measure Criteria of Multiple Sequences Alignment(MSA)

SHEN Shiyi(College of Mathematical Science, Nankai University, Tianjin 300071)  
The key of the alignment problem for the multiple biology sequences(DNA, RNA, or Pritein) is finding their similar part or stable region. So, the definition of the similarity measure or the cost function is a presupposition for the MSA. In this paper, we first give some rationality conditions of the similarity, then we give an optimization measure criterion using the Shannon entropy. This optimization measure criterion is a satisfaction to these similarity conditions.
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