RNASampler is a program that predicts common RNA secondary structure motifs in a group of related sequences.RNASampler finds the common structures between two sequences by probabilistically sampling aligned stems based on stem conservation calculated from intrasequence base pairing probabilities and intersequence base alignment probabilities. It iteratively updates these probabilities based on sampled structures and subsequently recalculates stem conservation using the updated probabilities. The iterative process terminates upon convergence of the sampled structures.
Stormo Lab in Department of Genetics, Washington University
- Vienna RNA Package
- Perl-5.8.8 or above
- IO-tty and Expect module for Perl
:: MORE INFORMATION
Xing Xu, Yongmei Ji, and Gary D. Stormo
RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment
Bioinformatics, August 2007; 23: 1883 – 1891.