Dhaka University Journal of Applied Science & Engineering

Dynamic programming algorithm for RNA secondary structure prediction including pseudoknot is efficient but expensive. On the other hand heuristic algorithm provide a good alternative for effective solution. We present SKnot, a heuristic algorithm for RNA secondary structure prediction including pseudoknot. Main idea of the algorithm is to find the promising candidate stems which can generate minimum free energy structure including pseudoknot. The algorithm is evaluated on 44 RNA sequences of various types. Experimental result suggest that SKnot predict secondary structure better in most cases in terms of sensitivity and specilicity compared to other well known algorithms like PKnotRG, NUPACK and DotKnot

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