On the Complexity of Protein Similarity Search under mRNA Structure Constraints
This paper addresses the complexity of a new problem associated with RNA secondary structure prediction. The issue is to identify an mRNA which has the secondary structure (=set of bonds) of a given mRNA, and the amino acid sequence it encodes has maximum similarity( defined below) to a given amino acid sequence. The problem is modeled as an optimization problem and a linear time algorithm is presented for the case when the given mRNA has a hairpin like secondary structure. Relevant extensions of this problem are shown to be NP-complete, and a factor 2 approximation algorithm is designed for the problem instances generated by the NP-completeness reduction.
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