A modification of Nussinov's algorithm

Question

[Yonatan]

Hi everyone, I came across with a question regarding the Nussinov algorithm(- a nucleic acid structure prediction algorithm used in computational biology to predict the folding of an RNA molecule) in my Bioinformatics class.

I've not manage to get to a solution and would love to get some help. The question is-

"Suggest an approach to change the Nussinov algorithm such that it supports the following biology assumption: Each edge is at least 2 stacked base-pairs length and each hairpin loops is at least 2 bases (single-strand) .

Suggest an algorithm that implement those assumptions and describe it well. The answer also has to be efficient and include the time complexity."

*** - Nussinov algorithm

THANK YOU very much in advance.

Jonathan.

[Joe]

Unfortunately it is against forum policy to answer homework/coursework questions. We can troubleshoot attempts you make at an answer and provide correction, but we cannot offer wholesale answers.