aut3D: Compute the Automorphisms of Mutational Events Between two...

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

Compute the Automorphisms of Mutational Events Between two Codon Sequences Represented in Z5^3.

Description

Given two codon sequences represented in the Z5^3 Abelian group, this function computes the automorphisms describing codon mutational events.

Usage

aut3D(
  seq = NULL,
  filepath = NULL,
  cube = c("ACGT", "TGCA"),
  cube_alt = c("CATG", "GTAC"),
  field = "GF5",
  start = NA,
  end = NA,
  chr = 1L,
  strand = "+",
  genetic_code = getGeneticCode("1"),
  num.cores = multicoreWorkers(),
  tasks = 0L,
  verbose = TRUE
)

Arguments

seq	An object from a DNAStringSet or DNAMultipleAlignment class carrying the DNA pairwise alignment of two sequences. The pairwise alignment provided in argument seq or the 'fasta' file filepath must correspond to codon sequences.
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, cube_alt	A character string denoting pairs of the 24 Genetic-code cubes, as given in references (2-3). That is, the base pairs from the given cubes must be complementary each other. Such a cube pair are call dual cubes and, as shown in reference (3), each pair integrates group.
field	A character string denoting the Galois field where the 3D automorphisms are estimated. This can be 'GF(4)' or 'GF(5)', but only 'GF(5)' is implemented so far.
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.
genetic_code	The named character vector returned by getGeneticCode or similar. The translation of codon into aminoacids is a valuable information useful for downstream statistical analysis. The standard genetic code is the default argument value applied in the translation of codons into aminoacids (see GENETIC_CODE_TABLE.
num.cores, tasks	Parameters for parallel computation using package BiocParallel-package: the number of cores to use, i.e. at most how many child processes will be run simultaneously (see bplapply and the number of tasks per job (only for Linux OS).
verbose	If TRUE, prints the progress bar.

Details

Automorphisms in Z5^3' are described as functions f(x) = A x mod Z5, where A is diagonal matrix, as noticed in reference (4).

Value

An object Automorphism-class with four columns on its metacolumn named: seq1, seq2, autm, and cube.

Author(s)

Robersy Sanchez (https://genomaths.com).

References

1. Sanchez R, Morgado E, Grau R. Gene algebra from a genetic code algebraic structure. J Math Biol. 2005 Oct;51(4):431-57. doi: 10.1007/s00285-005-0332-8. Epub 2005 Jul 13. PMID: 16012800. ( PDF).

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

3. 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.

4. 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. PDF.

Examples

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

## Automorphism on Z5^3
autms <- aut3D(seq = aln)
autms

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