title: RNAMAT: an efficient method to detect classes of RNA molecules and their structural features.
abstract: There is a growing appreciation for the diverse and important roles RNA molecules play in cellular function. RNAMAT is an approach based on matrix representation of all potential base-pairing of a set of sequences to reveal common secondary-structure features. When the RNA sequences come from one class, proper summation of these matrices exposes common structural features as demonstrated for tRNA and HACA-RNA. For C/D-RNA, a novel structural motif is suggested. Furthermore, it is demonstrated, in the case of tmRNA that the method can detect pseudo-knots which are structural motifs that are difficult to detect in other methods. When the sequences come from diverse sources, a specific clustering algorithm is suggested that is capable of detecting the common motifs. The algorithm is demonstrated in a case of a simulated example and in a real case derived from trypanosomes comparative RNomics study.
authors.affiliation: Dept. of Comput. Sci., Bar-Ilan Univ., Ramat-Gan, Israel.
authors.forename: Yair
authors.initials: Y
authors.lastname: Horesh
authors.forename: Amihood
authors.initials: A
authors.lastname: Amir
authors.forename: Shulamit
authors.initials: S
authors.lastname: Michaeli
authors.forename: Ron
authors.initials: R
authors.lastname: Unger