R: Synonymous codons

syncodons {seqinr} | R Documentation

## Synonymous codons

### Description

Returns all synonymous codons for each codon given

### Usage

    syncodons(codons, numcode = 1)

### Arguments

`codons` | A sequence of codons as generated by `splitseq`
`numcode` | The genetic code number as in `translate`

### Value

a list containing, for each codon given (list tags), all synonymous codons (including the original one)

### Author(s)

L. Palmeira, J.R. Lobry

### References

`citation("seqinr")`

### See Also

`synsequence`

### Examples

    #
    # The four synonymous codons for Alanine in the standard genetic code:
    #
    syncodons("ggg")
    #
    # With a sequence:
    #
    toycds <- s2c("tctgagcaaataaatcgg")
    syncodons(splitseq(toycds))
    #
    # Sanity check with the standard genetic code:
    #
    stdgencode <- structure(list(
      ttt = c("ttc", "ttt"),
      ttc = c("ttc", "ttt"),
      tta = c("cta", "ctc", "ctg", "ctt", "tta", "ttg"),
      ttg = c("cta", "ctc", "ctg", "ctt", "tta", "ttg"),
      tct = c("agc", "agt", "tca", "tcc", "tcg", "tct"),
      tcc = c("agc", "agt", "tca", "tcc", "tcg", "tct"),
      tca = c("agc", "agt", "tca", "tcc", "tcg", "tct"),
      tcg = c("agc", "agt", "tca", "tcc", "tcg", "tct"),
      tat = c("tac", "tat"),
      tac = c("tac", "tat"),
      taa = c("taa", "tag", "tga"),
      tag = c("taa", "tag", "tga"),
      tgt = c("tgc", "tgt"),
      tgc = c("tgc", "tgt"),
      tga = c("taa", "tag", "tga"),
      tgg = "tgg",
      ctt = c("cta", "ctc", "ctg", "ctt", "tta", "ttg"),
      ctc = c("cta", "ctc", "ctg", "ctt", "tta", "ttg"),
      cta = c("cta", "ctc", "ctg", "ctt", "tta", "ttg"),
      ctg = c("cta", "ctc", "ctg", "ctt", "tta", "ttg"),
      cct = c("cca", "ccc", "ccg", "cct"),
      ccc = c("cca", "ccc", "ccg", "cct"),
      cca = c("cca", "ccc", "ccg", "cct"),
      ccg = c("cca", "ccc", "ccg", "cct"),
      cat = c("cac", "cat"),
      cac = c("cac", "cat"),
      caa = c("caa", "cag"),
      cag = c("caa", "cag"),
      cgt = c("aga", "agg", "cga", "cgc", "cgg", "cgt"),
      cgc = c("aga", "agg", "cga", "cgc", "cgg", "cgt"),
      cga = c("aga", "agg", "cga", "cgc", "cgg", "cgt"),
      cgg = c("aga", "agg", "cga", "cgc", "cgg", "cgt"),
      att = c("ata", "atc", "att"),
      atc = c("ata", "atc", "att"),
      ata = c("ata", "atc", "att"),
      atg = "atg",
      act = c("aca", "acc", "acg", "act"),
      acc = c("aca", "acc", "acg", "act"),
      aca = c("aca", "acc", "acg", "act"),
      acg = c("aca", "acc",  "acg", "act"),
      aat = c("aac", "aat"),
      aac = c("aac", "aat"),
      aaa = c("aaa", "aag"),
      aag = c("aaa", "aag"),
      agt = c("agc", "agt", "tca", "tcc", "tcg", "tct"),
      agc = c("agc", "agt", "tca", "tcc", "tcg", "tct"),
      aga = c("aga", "agg", "cga", "cgc", "cgg", "cgt"),
      agg = c("aga", "agg", "cga", "cgc", "cgg", "cgt"),
      gtt = c("gta", "gtc", "gtg", "gtt"),
      gtc = c("gta", "gtc", "gtg", "gtt"),
      gta = c("gta", "gtc", "gtg", "gtt"),
      gtg = c("gta", "gtc", "gtg", "gtt"),
      gct = c("gca", "gcc", "gcg", "gct"),
      gcc = c("gca", "gcc", "gcg", "gct"),
      gca = c("gca", "gcc", "gcg", "gct"),
      gcg = c("gca", "gcc", "gcg", "gct"),
      gat = c("gac", "gat"),
      gac = c("gac", "gat"),
      gaa = c("gaa", "gag"),
      gag = c("gaa", "gag"),
      ggt = c("gga", "ggc", "ggg", "ggt"),
      ggc = c("gga", "ggc", "ggg", "ggt"),
      gga = c("gga", "ggc", "ggg", "ggt"),
      ggg = c("gga", "ggc", "ggg", "ggt")),

    .Names = c("ttt", "ttc", "tta", "ttg", "tct", "tcc", "tca", "tcg", "tat", "tac",
    "taa", "tag", "tgt", "tgc", "tga", "tgg", "ctt", "ctc", "cta",
    "ctg", "cct", "ccc", "cca", "ccg", "cat", "cac", "caa", "cag",
    "cgt", "cgc", "cga", "cgg", "att", "atc", "ata", "atg", "act",
    "acc", "aca", "acg", "aat", "aac", "aaa", "aag", "agt", "agc",
    "aga", "agg", "gtt", "gtc", "gta", "gtg", "gct", "gcc", "gca",
    "gcg", "gat", "gac", "gaa", "gag", "ggt", "ggc", "gga", "ggg"))
    #
    # Now the check:
    #
    currentresult <- syncodons(words(alphabet = s2c("tcag")))
    stopifnot(identical(stdgencode, currentresult))

[Package seqinr version 3.4-5 Index]