A binary coding method of RNA secondary structure and its application.

According to the three classifications of nucleotides, we introduce a sort of binary coding method of RNA secondary structures. On the basis of this representation, we can reduce a RNA secondary structure into three binary digit sequences. We also propose coding rules based on the exclusive-OR operation. Associating with the proposed coding rules, we can judge the mutation between bases or between base and base pair, and make sequence alignment easily. 2009 Wiley Periodicals, Inc.