The Single-Letter Amino Acid Code

Description

Named character vector mapping single-letter amino acid representations to 3-letter amino acid representations.

See Also

AAString, GENETIC_CODE

Examples

  ## See all the 3-letter codes
  AMINO_ACID_CODE

  ## Convert an AAString object to a vector of 3-letter amino acid codes
  aa <- AAString("LANDEECQW")
  AMINO_ACID_CODE[strsplit(as.character(aa), NULL)[[1]]]

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(Biostrings)
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Biostrings/AMINO_ACID_CODE.Rd_%03d_medium.png", width=480, height=480)
> ### Name: AMINO_ACID_CODE
> ### Title: The Single-Letter Amino Acid Code
> ### Aliases: AMINO_ACID_CODE
> ### Keywords: utilities data
> 
> ### ** Examples
> 
>   ## See all the 3-letter codes
>   AMINO_ACID_CODE
    A     R     N     D     C     Q     E     G     H     I     L     K     M 
"Ala" "Arg" "Asn" "Asp" "Cys" "Gln" "Glu" "Gly" "His" "Ile" "Leu" "Lys" "Met" 
    F     P     S     T     W     Y     V     U     O     B     J     Z     X 
"Phe" "Pro" "Ser" "Thr" "Trp" "Tyr" "Val" "Sec" "Pyl" "Asx" "Xle" "Glx" "Xaa" 
> 
>   ## Convert an AAString object to a vector of 3-letter amino acid codes
>   aa <- AAString("LANDEECQW")
>   AMINO_ACID_CODE[strsplit(as.character(aa), NULL)[[1]]]
    L     A     N     D     E     E     C     Q     W 
"Leu" "Ala" "Asn" "Asp" "Glu" "Glu" "Cys" "Gln" "Trp" 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>