Figure 1.

Averaged base-paring probability matrices and DAG kernels using the dynamic programming technique enable us to calculate profile-profile stem kernels for multiple alignments of RNA sequences. (a) Given a pair of multiple alignments, (b) Calculate the base-paring probability matrices for each sequence in the multiple alignments and average these base-pairing probabilities with respect to the columns of each alignment. (c) Build a DAG for the averaged base-pairing probability matrix, where each vertex corresponds to a base pair whose probability is above a predefined threshold. (d) Calculate a kernel value for a pair of DAGs for the multiple alignments by using the DAG kernel and the dynamic programming technique.