RNAv (RNA secondary structure variation) is a program that searches for RNA secondary structure variations based on the notion of a structure graph to specify the consensus structure of an RNA family.The model for profiling the consensus structure of an RNA family is a conformational graph that specifies the topology of the consensus fold and relationship among helices and unpaired loops. Individual helices and loops are modeled with a restricted Covariance Model and profile HMM, respectively. The fold topology, helices, and loops are trained with an input pasta file that contains a multiple structural alignment for a set of training RNA sequences.
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Huang, Z., Malmberg, R., Mohebbi M., and Cai, L. (2010)
RNAv: Non-coding RNA Secondary Structure Variation Search via Graph Homomorphism
Proceedings of Computational Systems Bioinformatics Conference (CSB 2010), August, 2010. Vol. 9, p. 56-69.