MicroRNA IDs to Minimum Fold Energy

Description

mirbaseMFE is an R object that provides mappings between microRNA identifiers and the Minimum Fold Energy of the folded precursor (stem-loop sequence).

Details

Each microRNA identifier maps to a unique numeric value representing the Minimum Fold Energy of the folded precursor (stem-loop sequence) computed by the RNAfold program from the ViennaRNA suite http://www.tbi.univie.ac.at/~ivo/RNA/.

A graphical representation of the folded sequence can be found by using mirbaseHAIRPIN.

Source: miRBase (Version: 19) ftp://mirbase.org/pub/mirbase/CURRENT/ With a date stamp from the source of: 01 Aug 2012

References

Hofacker IL, Stadler PF. Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics. 2006 May 15; 22(10):1172-6. http://www.ncbi.nlm.nih.gov/pubmed/16452114

See Also

mirbaseHAIRPIN

Examples

    x <- mirbaseMFE
    # Get the microRNA identifiers that are mapped to a MFE
    mapped_keys <- mappedkeys(x)
    # Convert to a list
    xx <- as.list(x[mapped_keys])
    if(length(xx) > 0) {
        # Get the MFE for the first five entries
        xx[1:5]
    }