How can I search for known miRNAs?

The search page allows you to search the database in a number of ways. You can search by identifier (e.g. "let-7" or "miR-36") or keyword (e.g. "elegans") in the top panel. The bottom panel allows you to perform BLASTN and SSEARCH searches of a query sequence against the database of known miRNAs. You can choose to search the precursor sequences or just the mature miRNAs. Choose BLASTN to search for a miRNA in a longer sequence. SSEARCH is useful for finding a short sequence within the library of miRNAs (for instance, find a short motif in a miRNA or precursor stem-loop, or find mature sequences that are related to your query). The search may take a couple of minutes. The results are returned in table format with alignments of query and database hit shown below.

You can also browse the database of miRNAs from the browse pages. From this page you can access published miRNAs by organism.

From the results of and type of search or browse you can click on an miRNA name to access the entry page. This page contains information about the miRNA gene of interest and depicts the precusor sequence with the mature miRNA sequence highlighted. The folded precursor structure is computed using the RNAfold program from the ViennaRNA suite. Limitations of the ascii depiction mean that for complex structures, such as some of the plant precursors, only base pairing interactions of the first helix are shown. The entry table also contains links to publications describing the identification of the miRNA.