codon_coord: Codon coordinates on a given a given Abelian group...

In genomaths/GenomAutomorphism: Compute the automorphisms between DNA's Abelian group representations

Codon coordinates on a given a given Abelian group representation.

Description

Given a string denoting a codon or base from the DNA (or RNA) alphabet and a genetic-code Abelian group as given in reference (1).

Usage

codon_coord(codon = NULL, ...)

## S4 method for signature 'BaseGroup'
codon_coord(codon, group = NULL)

## S4 method for signature 'DNAStringSet_OR_NULL'
codon_coord(
  codon = NULL,
  filepath = NULL,
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  group = c("Z4", "Z5", "Z64", "Z125", "Z4^3", "Z5^3"),
  start = NA,
  end = NA,
  chr = 1L,
  strand = "+"
)

## S4 method for signature 'matrix_OR_data_frame'
codon_coord(
  codon,
  cube = c("ACGT", "AGCT", "TCGA", "TGCA", "CATG", "GTAC", "CTAG", "GATC", "ACTG",
    "ATCG", "GTCA", "GCTA", "CAGT", "TAGC", "TGAC", "CGAT", "AGTC", "ATGC", "CGTA",
    "CTGA", "GACT", "GCAT", "TACG", "TCAG"),
  group = c("Z64", "Z125", "Z4^3", "Z5^3")
)

Arguments

codon	An object from BaseGroup-class (generated with function base_coord), DNAStringSet or from DNAMultipleAlignment class carrying the DNA pairwise alignment of two sequences.
...	Not in use.
group	A character string denoting the group representation for the given base or codon as shown in reference (2-3).
filepath	A character vector containing the path to a file in fasta format to be read. This argument must be given if codon & base arguments are not provided.
cube	A character string denoting one of the 24 Genetic-code cubes, as given in references (2-3).
start, end, chr, strand	Optional parameters required to build a GRanges-class. If not provided the default values given for the function definition will be used.

Details

Symbols "-" and "N" usually found in DNA sequence alignments to denote gaps and missing/unknown bases are represented by the number: '-1' on Z4 and '0' on Z5. In Z64 the symbol 'NA' will be returned for codons including symbols "-" and "N".

This function returns a GRanges-class object carrying the codon sequence(s) and their respective coordinates in the requested Abelian group or simply, when group = 'Z5^3' 3D-coordinates, which are derive from Z5 as indicated in reference (3). Notice that the coordinates can be 3D or just one-dimension ("Z64" or "Z125"). Hence, the pairwise alignment provided in argument codon must correspond to codon sequences.

Value

A CodonGroup-class object.

Author(s)

Robersy Sanchez https://genomaths.com

References

1. Robersy Sanchez, Jesus Barreto (2021) Genomic Abelian Finite Groups. doi: 10.1101/2021.06.01.446543

2. M. V Jose, E.R. Morgado, R. Sanchez, T. Govezensky, The 24 possible algebraic representations of the standard genetic code in six or in three dimensions, Adv. Stud. Biol. 4 (2012) 119-152.PDF.

3. R. Sanchez. Symmetric Group of the Genetic-Code Cubes. Effect of the Genetic-Code Architecture on the Evolutionary Process MATCH Commun. Math. Comput. Chem. 79 (2018) 527-560.

See Also

Symmetric Group of the Genetic-Code Cubes.

codon_matrix, base_coord and base2int.

Examples

## Load a pairwise alignment
data("aln", package = "GenomAutomorphism")
aln

## DNA base representation in the Abelian group Z5
bs_cor <- codon_coord(
    codon = aln,
    cube = "ACGT",
    group = "Z5"
)
bs_cor ## 3-D coordinates


## DNA base representation in the Abelian group Z64
bs_cor <- codon_coord(
    codon = aln,
    cube = "ACGT",
    group = "Z64"
)
bs_cor

## Giving a matrix of codons
codon_coord(base2codon(x = aln))

genomaths/GenomAutomorphism documentation built on Dec. 12, 2024, 2:12 p.m.