Welcome to Vir-Mir database, a database containing predicted viral miRNA candidate hairpins. This database is constructed and maintained by the Transcriptome Discovery Lab(TDL), Institute of BioMedical Science, Academia Sinica, Taipei, Taiwan.

We have previously identified human intronic microRNA as well as zebrafish microRNA. The microRNA hairpin discovery pipeline was also applied to discover viral encoded microRNAs. All viral genomes were obtain from NCBI. The classification of virus is based on the taxonomy table of NCBI (Jun, 2006). Totally, the genomes of 2266 viruses were analyzed. Users may query the putative miRNA hairpins of a specific viral species by the hierarchical menu or by search function using the GenBank Identifier or RefSeq accession number(e.g. 30844336 or NC_003663 for Cowpox virus). In addition, users can also search for the putative target genes of a particular viral miRNA hairpins by a RNAhybrid service link. The 3'-UTR regions of human, mouse, rat, zebrafish, arabidopsis and rice genes are available for search. RNAhybrid program is kindly provide by Dr. Rehmsmeier (Original paper:"Fast and effective prediction of microRNA/target duplexes.").

If you use this database for any research that results in a publication, please cite:
Li SC, Shiau CK, Lin WC. 2007. Vir-Mir db: prediction of viral microRNA candidate hairpins. Nucleic Acids Research. Advance Access published August 15, 2007, doi:10.1093/nar/gkm610.
Li SC, Pan CY, Lin WC. 2006. Bioinformatic discovery of microRNA precursors from human ESTs and introns. BMC Genomics 7:164.

Optional help : Figure-based instruction | Text-based instruction

Any comments and questions are welcome. Please send to Wen-chang Lin via wenlin@ibms.sinica.edu.tw.

  Predicted viral microRNA hairpins - classified by NCBI Taxonomy list:
( Accumulated Numbers of Hairpin Candidates )
    Deltavirus ( 0 )
    dsDNA viruses, no RNA stage ( 26339 )
    dsRNA viruses ( 379 )
    environmental samples ( 0 )
    Retro-transcribing viruses ( 386 )
    Satellites ( 59 )
    ssDNA viruses ( 410 )
    ssRNA negative-strand viruses ( 167 )
    ssRNA positive-strand viruses, no DNA stage ( 2325 )
    unclassified viruses ( 374 )

  Supplementary Information:
    Known virus microRNAs extracted from MiRBase

  Search portal: (eg. NC_007605; Search by GenBank Id., RefSeq Acc., or viral scientific name)
    

Target gene prediction:

  RNAhybrid Service Page
  RNAhybrid Service Page - Job Progress

Other microRNA predicted dataset by TDL:

  1.Predicted Human intronic and EST microRNAs

  2.Predicted Zebrafish microRNAs
     EST miRNA
     Intronic miRNA
     Genomic miRNA
     Known miRNA in miRBase