MicroRNA IDs to Hairpin

Description

mirbaseHAIRPIN is an R object that provides mappings between microRNA identifiers and an ASCII representation of the the folded precursor (stem-loop sequence).

Details

Each microRNA identifier maps to a character string. The mature microRNA(s) sequence are highlighted in capital letters.

The representation was created the RNAfold program from the ViennaRNA suite http://www.tbi.univie.ac.at/~ivo/RNA/. Extra information include the minimum free energy ('MFE') which can be found by using mirbaseMFE and the position on the sequence of mature mirna(s) which can be found by using mirbaseMATURE.

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

Examples

    x <- mirbaseHAIRPIN
    # hairpin representation sequences of all microRNAs
    mirnaHairpin <- mget(mappedkeys(x), x)
    # print first one
    cat(mirnaHairpin[[1]], "\n")