Abstract
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.
Partially supported by the DFG (national program SPP 1087 “Selenoprotein — Biochemische Grundlagen und klinische Bedeutung”)
Supported by DFG Grant No. Jo 291/2-1.
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Backofen, R., Narayanaswamy, N., Swidan, F. (2002). On the Complexity of Protein Similarity Search under mRNA Structure Constraints. In: Alt, H., Ferreira, A. (eds) STACS 2002. STACS 2002. Lecture Notes in Computer Science, vol 2285. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45841-7_22
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DOI: https://doi.org/10.1007/3-540-45841-7_22
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