D184–D189 Nucleic Acids Research, 2008, Vol. 36, Database issue doi:10.1093/nar/gkm610 Published online 15 August 2007 Vir-Mir db: prediction of viral microRNA candidate hairpins Sung-Chou Li1, Cheng-Kai Shiau2 and Wen-chang Lin1,2,* 1Institute of BioMedical Informatics, National Yang-Ming University, Taipei 112 and 2Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, Republic of China Received June 15, 2007; Revised July 17, 2007; Accepted July 26, 2007 ABSTRACT MicroRNAs have been found in various organisms and play essential roles in gene expression regula- tion of many critical cellular processes. Large-scale computational prediction of miRNAs has been conducted for many organisms using known geno- mic sequences; however, there has been no such effort for the thousands of known viral genomes. Some viruses utilize existing host cellular pathways for their own benefit. Furthermore, viruses are capable of encoding miRNAs and using them to repress host genes. Thus, identifying potential miRNAs in all viral genomes would be valuable to virologists who study virus–host interactions. Based on our previously reported hairpin secondary struc- ture and feature selection filters, we have examined the 2266 available viral genome sequences for putative miRNA hairpins and identified 33 691 hair- pin candidates in 1491 genomes. Evaluation of the system performance indicated that our discovery pipeline exhibited 84.4% sensitivity. We established an interface for users to query the predicted viral miRNA hairpins based on taxonomic classification, and a host target gene prediction service based on the RNAhybrid program and the 3’-UTR gene sequences of human, mouse, rat, zebrafish, rice and Arabidopsis. The viral miRNA prediction data- base (Vir-Mir) can be accessed via http:// alk.ibms.sinica.edu.tw. INTRODUCTION MicroRNAs (miRNAs) are endogenous non-protein- coding RNAs that are 22-nt long. They negatively regulate gene expression by complementary binding to the 30-UTR regions of target genes (1). Since the ﬁrst discovery of miRNA in Caenorhabditis elegans, thousands of miRNAs have been computationally and/or experi- mentally identiﬁed in many organisms, including mammals, invertebrates, insects and plants (2). It has been shown that miRNAs can function in various physiological pathways. Plant miRNAs can regulate development in embryos, leaves and ﬂoral meristems (3,4). Mammalian miRNAs participate not only in developmental regulation (5) but also in pathogenesis if they are dysfunctional (6). Even with limited informa- tion about miRNA gene structures and their target genes’ recognition selections, several genome-wide bioinfor- matics approaches have been recently employed to identify these important molecules (7–9). Establishing such a bioinformatic resource for miRNA will be beneﬁcial for daily experimental research in the biological laboratories. Similar to many eukaryotic organisms, viruses also encode miRNAs (10,11). To date, at least 82 viral- associated miRNAs have been identiﬁed from eight diﬀerent viruses (2). Because viruses are often parasitic, these viral miRNAs may target important host genes to reduce the host cell defense and to control host cell biogenesis. Human herpes virus 4 (Epstein-Barr virus, EBV) represses several host genes, including those encoding B cell-speciﬁc chemokines and cytokines, tran- scriptional regulators and components of signal transduc- tion pathways, by means of virus-encoded miRNAs (11). Moreover, HIV-1 also has been proposed to enhance viral infection capability by repressing host immune system genes via speciﬁc HIV viral miRNAs (10). MOTIVATION It would be beneﬁcial for biomedical researchers who study virus–host interactions to identify potential viral miRNAs and their target genes in hosts. Although a new database collecting viral gene targets of host miRNAs has been reported recently (12), but there is no genome- wide miRNA prediction for all completed viral genome sequences. We have modiﬁed our previous miRNA discovery pipeline to predict viral miRNA hairpins (13). Here, we present our research eﬀort on candidate hairpin discovery of virus-encoded miRNAs from all virus genomes available from the National Center for *To whom correspondence should be addressed. Tel: +886226523967; Fax: 886227827654; Email: wenlin@ibms.sinica.edu.tw 2007 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.