Webserver to compute b> Expected 5-3 distance in RNAb>
The C program averageDistance5to3.c and its Python prototype distance5to3.py are efficient and exact computations of the expected distance between 5' and 3' ends of all secondary structures for a given RNA sequence. The expectation or average is taken with respect to the Boltzmann probability exp(-E(S)/RT)/Z, where E(S) is the Turner energy for secondary structure S, R the universal gas constant, T absolute temperature, and Z the partition function.
If you use our code or this server for your work, please consider citing the paper:
Expected distance between terminal nucleotides of RNA secondary structures. P. Clote, Y. Ponty, J.-M. Steyaert. J Math Biol. 2012 Sep;65(3):581-99. Epub 2011 Oct 9.Supplementary information is here.