RSSVM (RNA Sampler + Support Vector Machine) employs Support Vector Machines (SVM) for efficient identification of functional RNA motifs from random RNA structures. It uses a set of distinctive features to represent the common RNA secondary structure and structural alignment predicted by RNA Sampler, a tool for accurate RNA common structure prediction, and is trained with functional RNAs from a variety of bacterial RNA motif/gene families covering a wide range of sequence identities.
Stormo Lab in Department of Genetics, Washington University
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Xing Xu, Yongmei Ji, and Gary D. Stormo
Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines
PLoS Computational Biology, in revision, Sept 2008.