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ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs
1 Graduate Program in Bioinformatics, Seoul National University Seoul 151-744, Korea 2 Center for Bioinformation Technology (CBIT), Seoul National University Seoul 151-744, Korea 3 Biointelligence Laboratory, School of Computer Science and Engineering, Seoul National University Seoul 151-744, Korea
*To whom correspondence should be addressed. Tel: +82 2 880 1847; Fax: +82 2 875 2240; Email: btzhang{at}bi.snu.ac.kr
Received February 14, 2006. Revised March 12, 2006. Accepted April 13, 2006.
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/.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
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