RNAv: Search Genomes for RNA secondary structure variation


RNAv (RNA secondary structure variation) is a profile based RNA secondary structure variation search program that detects distant ncRNA structural homologs. 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.


RNAv is coded in C++ and compiled and tested on several systems, including Desktop Linux computers, a Linux cluster, and a SUN workstation running SunOS 5.1. The following downloadable version is for Linux platform.

Related Software

RNATOPS: A tool for fast and accurate search for non-coding RNA pseudoknot structures in genomes.

RNATOPS-W: This is a web server version of RNATOPS (based on rnatops.v1.1). It incorporates a filtering function for search speed-up and comes with the options of automatic (HMM) filter selection and manual filter selection by the user.


    [Huang, et al., 2010] 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.

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