An exploration of individual RNA structural elements in RNA gene finding

Abstract

This paper explores the use of RNA structural elements for RNA gene finding. A classification experiment is performed in which several support vector machine models, based on the properties of individual RNA secondary structure elements, are trained and tested, revealing the structural elements which have properties useful for RNA gene finding. The study finds that the external loop and structure elements with classification accuracies of over 84% and the stemloop, hairpin, and tail elements with classification accuracies around 70% are the most likely structural elements to be successfully exploited by future RNA gene finders.