Hello everyone, part of my master thesis needs to compute partition function for quite a big alignment of RNA sequences (16 thousand, probably more for other data sets). Basically what I need is to compute base pair probabilities for every sequence in this alignment. I tried RNAfold, but I could not retrieve base pair probabilities for them (it returned only dot plot - I need float numeric values), plus as an output, it computed as many files as many sequences were in my input fasta file and I would like to have my results in a file. I also tried RNAstructure software, but single run of this program was only for one (first) sequence in my file, and I would rather not split my input date into 16 thousands files.

My question to You all is - do You know any software that could: - count base pair probabilities (return float <0.0, 1.0> by counting partition function for big RNA sequences alignment; - and that could return a result in ONE file;

Thank You all in advance, hopefully, some of You have some experience with such a problem.