title: Modeling alternate RNA structures in genomic sequences.
abstract: We introduce the concept of RNA multistructures, which is a formal grammar-based framework specifically designed to model a set of alternate RNA secondary structures. Such alternate structures can either be a set of suboptimal foldings, or distinct stable folding states, or variants within an RNA family. We provide several such examples and propose an efficient algorithm to search for RNA multistructures within a genomic sequence.
authors.affiliation: LIFL, UMR 8022 CNRS, University of Lille , and Inria Lille, Villeneuve d'Ascq, France .
authors.forename: Azadeh
authors.initials: A
authors.lastname: Saffarian
authors.forename: Mathieu
authors.initials: M
authors.lastname: Giraud
authors.forename: Hélène
authors.initials: H
authors.lastname: Touzet
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000737:chemistry; D016678:Genome; D006801:Humans; D055029:Inverted Repeat Sequences; D008958:Models, Molecular; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding; D012329:RNA, Bacterial / Q000737:chemistry; D000077278:RNA, Mitochondrial; D012343:RNA, Transfer / Q000737:chemistry*; D043262:Ribonuclease P / Q000737:chemistry; D058928:Riboswitch
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D000077278:RNA, Mitochondrial; D058928:Riboswitch; D012313:RNA; D012343:RNA, Transfer; D043262:Ribonuclease P
keywords: RNA; algorithms; alignment; dynamic programming; secondary structure