RNATOPS (RNA via Tree decOmPoSition) is a program that searches for RNA secondary structures 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.
- Windows / MacOsX / Linux
- C++ Complier
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Huang, Z., Wu, Y., Robertson, J., Feng, L., Malmberg, R., and Cai, L. (2008)
Fast and accurate search for non-coding RNA pseudoknot structures in genomes,