How to run RNAmutants

Simple! Follow the steps below.

• Paste your RNA sequence in FASTA format in the first box.
• Choose upper bound K for number of mutant nucleotide positions.
• Submit your request by clicking on the "Submit" button!

RNAmutants will compute the partition function Z_k, for all 0 ≤ k &le K, where K is the user-specified upper bound. In addition, RNAmutants computes a graph of the expected energy as a function of the number k of mutated nucleotide positions (available via a hot link).

To additionally obtain the k-superoptimal secondary structures, select the option to receive these by email (this computation takes substantial time, hence your results will be returned by email). Your email address is necessary in this case.

NOTE: If the RNA sequence is larger than 50 nt., then computation time exceeds the time that a browser window can wait for results, hence your results will be sent by email. In this case, you must enter an e-mail address.

WARNING

• Letting n denote the length of the RNA sequence, the underlying algorithm for this computation runs in O(n² K) space and O(n³ K) time. Due to time and space constraints, the RNAmutants web server requires that n not exceed 300, and that n² K be bounded by 1 million.
• In the current algorithm, energy is a variant of Nussinov-Jacobson energy, where GC, AU, GU base pairs respectively contribute a value of -3,-2,-1. In subsequent work, the Turner energy model will be employed.