Manual

Enter an RNA sequence, along with the maximum number of mutations to be considered (algorithm scales quadratically in number of mutations), the desired number of RNA sequence-structure pairs to be sampled from the Boltzmann ensemble, and the temperature in Celsius. Enter your email (required) and either paste an RNA sequence (with no FASTA comment) or upload a file containing an RNA sequence.

For each value 0 ≤ k ≤ Kmax, RNAmutants web server computes the partition function Z(k) = sum exp(-E(s,S)/RT) where the sum is taken over all sequence-structure pairs s,S, where s is a k-point mutant of the input sequence, and S is a secondary structure for sequence s. The Boltzmann partition function values are subsequently used to sample a user-defined number of sequence-structure pairs from the low energy ensemble.

Additionally, for each value of k, RNAmutants computes the sequence-structure pair s,S, such that secondary structure S for k-point mutant s has the lowest free energy over all k-point mutant sequence-structure pairs.

If your RNA sequence exceeds a modest default length (40 nt) or the maximum number of mutations exceeds a default value (5 mutations), then output will be returned by email.

NOTE: RNAmutants run time is O(Kmax2*n3). Currently, if sequence length (N) times the upper bound for number of permitted mutations (K) exceeds 200, then results are emailed to the user, since large jobs require too many resources for interactive runs. In such cases, the loading page indicates the message

This might take a while. Results will be emailed.
at the bottom, just above a link to take the user to the Results Page. Results will be subsequently be emailed to the user.

EXAMPLES

  1. 51 nt. RNA sequence, which is the 3' untranslated regionfrom mRNA with NCBI accession code MUSGBPA. Output from RNAmutants summarized here.
  2. 101 nt. SAM riboswitch sequence from Rfam, with EMBL accession code AP004597.1/118941-119041; output from RNAmutants summarized here.
  3. RNAmutants analysis including Mutability profile of 48 nt HAR1 region, where the number of mutations ranges from 1 to 40. HAR1 is part of the novel RNA gene HAR1F (39), expressed in Cajal-Retzius neurons in the developing human neocortex, a gene believed to show significant evolutionary acceleration. Sequence taken from Pollard et al., Nature 2006. Results are here.

Output from RNAmutants web engine for 51 nt. 3' UTR of mRNA MUSGBPA:

Output from RNAmutants web engine for 101 nt SAM riboswitch with EMBL accession code AP004597.1/118941-119041.