title: Computational methods in noncoding RNA research.
abstract: Non protein-coding RNAs (ncRNAs) are a research hotspot in bioinformatics. Recent discoveries have revealed new ncRNA families performing a variety of roles, from gene expression regulation to catalytic activities. It is also believed that other families are still to be unveiled. Computational methods developed for protein coding genes often fail when searching for ncRNAs. Noncoding RNAs functionality is often heavily dependent on their secondary structure, which makes gene discovery very different from protein coding RNA genes. This motivated the development of specific methods for ncRNA research. This article reviews the main approaches used to identify ncRNAs and predict secondary structure.
authors.affiliation: Institute of Mathematics and Statistics, University of Sao Paulo, Sao Paulo, SP, Brazil. ariane@ime.usp.br
authors.forename: Ariane
authors.initials: A
authors.lastname: Machado-Lima
authors.forename: Hernando A
authors.initials: HA
authors.lastname: del Portillo
authors.forename: Alan Mitchell
authors.initials: AM
authors.lastname: Durham
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000737:chemistry* / Q000235:genetics*; D013816:Thermodynamics