Question: Computing The Baseline Nussinov Score For Biological Significance
gravatar for biostudent
6.6 years ago by
biostudent30 wrote:

I know how to compute the Nussinov score for a given RNA sequence, but I don't know whether any score I compute is biologically significant. How do I go about computing a baseline score using the Nussinov algorithm such that any score above this baseline, I know is biologically significant?

rna sequencing • 1.5k views
ADD COMMENTlink modified 5.4 years ago by Biostar ♦♦ 20 • written 6.6 years ago by biostudent30
gravatar for Andreas
6.6 years ago by
Andreas2.4k wrote:

One way of computing a 'background' to compare a score to, is be to shuffle/permute your RNA sequence and recompute the score for each such 'randomized' sequence.

I assume this is for illustrational/educational purposes only and that you know about the efficient algorithms and implementations which are based on proper thermodynamics models, e.g. the Vienna RNA package.


ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by Andreas2.4k
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