classiﬁcation and arrangement of the viral candidates are according to the taxonomy table of NCBI, so users can query the viral miRNAs more easily. Users may query the putative miRNAs from a speciﬁc virus by using the Figure 2. Expanded view of taxonomy table. The classiﬁcation and arrangement of viral miRNA candidate hairpins are based on the taxonomy table of NCBI. The numbers in the right parentheses of each classiﬁcation level indicate the numbers of candidate hairpins found in those levels. By clicking on a link, users can see the expanded table. The numbers in parentheses indicate the number of candidate hairpins found in that particular viral genome. Nucleic Acids Research, 2008, Vol. 36, Database issue D187 hierarchical menu or by using the simple search function. A keyword search can be performed, but users are recommended to use it with the GenBank identiﬁer or RefSeq accession number for better search result, e.g. 30844336 or NC_003663 for Cowpox virus. The numbers in the right parentheses of each classiﬁca- tion level indicate the numbers of candidate hairpins found in that level. For example, Atadenovirus has 18 candidate hairpins, which are cumulated from its four sub-classes of viruses, including Bovine adenovirus, Duck adenovirus A, Ovine adenovirus D and Possum adeno- virus. We identiﬁed 16 candidate hairpins from Duck adenovirus A and no candidate hairpin from Bovine adenovirus D. In some cases, like Bovine adenovirus 4, 5, 8 and Possum adenovirus, we did not record the number of candidate hairpins in their right parentheses, which means there are no genomic sequences available for analysis at these classiﬁcation levels. After selecting a speciﬁc virus type, as illustrated in Figure 3 for human herpes virus 4, users may further sort the candidate hairpins according to the miRNA genomic location (default), score by Srnaloop, or core mfe by RNAfold. Moreover, for known pre-miRNAs, the sequences and locations of mature miRNAs are shown according to the known miRNA information. For example, both ebv-mir-BHRF1-1 and ebv-mir-BHRF1-3 have only one mature miRNA in their 50 arms. Figure 3. Viral miRNA candidate hairpin web interface. Here, users can view all the predicted viral miRNA hairpin information for a particular virus. They may sort the candidate hairpins according to genomic location (default), score calculated by Srnaloop or core mfe calculated by RNAfold. The YP accession number in the NP reference protein column denotes the protein-coding ORF sequence overlapped by this candidate hairpin. Click the ﬁeld header to sort on a ﬁeld. Click it again to reverse the sorted list.