title: ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.
abstract: ProMiR is a web-based service for the prediction of potential microRNAs (miRNAs) in a query sequence of 60-150 nt, using a probabilistic colearning model. Identification of miRNAs requires a computational method to predict clustered and nonclustered, conserved and nonconserved miRNAs in various species. Here we present an improved version of ProMiR for identifying new clusters near known or unknown miRNAs. This new version, ProMiR II, integrates additional evidence, such as free energy data, G/C ratio, conservation score and entropy of candidate sequences, for more controllable prediction of miRNAs in mouse and human genomes. It also provides a wider range of services, e.g. the prediction of miRNA genes in long nonrelated sequences such as viral genomes. Importantly, we have validated this method using several case studies. All data used in ProMiR II are structured in the MySQL database for efficient analysis. The ProMiR II web server is available at http://cbit.snu.ac.kr/~ProMiR2/.
authors.affiliation: Graduate Program in Bioinformatics, Seoul National University, Seoul 151-744, Korea.
authors.forename: Jin-Wu
authors.initials: JW
authors.lastname: Nam
authors.forename: Jinhan
authors.initials: J
authors.lastname: Kim
authors.forename: Sung-Kyu
authors.initials: SK
authors.lastname: Kim
authors.forename: Byoung-Tak
authors.initials: BT
authors.lastname: Zhang
mesh_terms: D000818:Animals; D001483:Base Sequence; D017124:Conserved Sequence; D016679:Genome, Viral; D023281:Genomics / Q000379:methods; D006801:Humans; D020407:Internet; D051379:Mice; D035683:MicroRNAs / Q000235:genetics*; D015233:Models, Statistical; D005810:Multigene Family; D051381:Rats; D012984:Software; D014584:User-Computer Interface
chemical_list: D035683:MicroRNAs