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")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(mirbase.db)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mirbase.db/mirbaseHAIRPIN.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mirbaseHAIRPIN
> ### Title: MicroRNA IDs to Hairpin
> ### Aliases: mirbaseHAIRPIN
> ### Keywords: data
> 
> ### ** Examples
> 
>     x <- mirbaseHAIRPIN
>     # hairpin representation sequences of all microRNAs
>     mirnaHairpin <- mget(mappedkeys(x), x)
>     # print first one
>     cat(mirnaHairpin[[1]], "\n")
------uaca    gga             U              ---  aaua 
          cugu   uccggUGAGGUAG AGGUUGUAUAGUUu   gg    u
          ||||   ||||||||||||| ||||||||||||||   ||     
          gaca   aggcCAUUCCAUC UUUAACGUAUCAAG   cc    u
agcuucucaa    --g             U              Ugg  acca  
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>