title: Knowledge-based reasoning to annotate noncoding RNA using multi-agent system.
abstract: Noncoding RNAs (ncRNAs) have been focus of intense research over the last few years. Since characteristics and signals of ncRNAs are not entirely known, researchers use different computational tools together with their biological knowledge to predict putative ncRNAs. In this context, this work presents ncRNA-Agents, a multi-agent system to annotate ncRNAs based on the output of different tools, using inference rules to simulate biologists' reasoning. Experiments with data from the fungus Saccharomyces cerevisiae allowed to measure the performance of ncRNA-Agents, with better sensibility, when compared to Infernal, a widely used tool for annotating ncRNA. Besides, data of the Schizosaccharomyces pombe and Paracoccidioides brasiliensis fungi identified novel putative ncRNAs, which demonstrated the usefulness of our approach. NcRNA-Agents can be be found at: http://www.biomol.unb.br/ncrna-agents.
authors.affiliation: * Department of Computer Science, University of Brasília, Campus Universitário Darcy Ribeiro Prédio CIC/EST, ASA Norte, Brasília-DF,CEP: 70910-900, Brazil.
authors.forename: Wosley C
authors.initials: WC
authors.lastname: Arruda
authors.affiliation: * Department of Computer Science, University of Brasília, Campus Universitário Darcy Ribeiro Prédio CIC/EST, ASA Norte, Brasília-DF,CEP: 70910-900, Brazil.
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Souza
authors.affiliation: * Department of Computer Science, University of Brasília, Campus Universitário Darcy Ribeiro Prédio CIC/EST, ASA Norte, Brasília-DF,CEP: 70910-900, Brazil.
authors.forename: Célia G
authors.initials: CG
authors.lastname: Ralha
authors.affiliation: * Department of Computer Science, University of Brasília, Campus Universitário Darcy Ribeiro Prédio CIC/EST, ASA Norte, Brasília-DF,CEP: 70910-900, Brazil.
authors.forename: Maria Emilia M T
authors.initials: ME
authors.lastname: Walter
authors.affiliation: † Leônidas and Maria Deane Research Center (Fiocruz Amazônia), Rua Teresina, 476 Adrianópolis, Manaus-AM, CEP: 69027-070, Brazil.
authors.forename: Tainá
authors.initials: T
authors.lastname: Raiol
authors.affiliation: ‡ Department of Cellular Biology, Institute of Biology, University of Brasília, Campus Universitário Darcy Ribeiro, Prédio do Institute de Biologia, ASA Norte, Brasília-DF,CEP: 70910-900, Brazil.
authors.forename: Marcelo M
authors.initials: MM
authors.lastname: Brigido
authors.affiliation: § Department of Computer Science and the Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107, Leipzig, Germany.
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D058977:Molecular Sequence Annotation / Q000379:methods; D010228:Paracoccidioides / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012568:Schizosaccharomyces / Q000235:genetics; D012984:Software
chemical_list: D022661:RNA, Untranslated
keywords: Noncoding RNA annotation; fungi ncRNA annotation; knowledge-based reasoning; multi-agent system