GitHub - genomaths/GenomAutomorphism: An R package to compute the autimorphisms between pairwise aligned DNA sequences represented as elements from a Genomic Abelian group as described in the paper Genomic Abelian Finite Groups (original) (raw)

GenomAutomorphism

Robersy Sanchez
Department of Biology. Eberly College of Science.
Pennsylvania State University, University Park, PA 16802
genomicmath@gmail.com
ORCID: orcid.org/0000-0002-5246-1453

Overview

This is a R package to compute the automorphisms between pairwise aligned DNA sequences represented as elements from a Genomic Abelian group as described in the paper Genomic Abelian Finite Groups. In a general scenario, whole chromosomes or genomic regions from a population (from any species or close related species) can be algebraically represented as a direct sum of cyclic groups or more specifically Abelian _p_-groups. Basically, we propose the representation of multiple sequence alignments (MSA) of length N as a finite Abelian group created by the direct sum of homocyclic Abelian group of prime-power order:

G = (ℤ_p_1_α_1)_n_1 ⊕ (ℤ_p_1_α_2)n_2 ⊕ … ⊕ (ℤ_p k α k)n k

Where, the p i_’s are prime numbers, α i ∈ ℕ and ℤ_p i α i is the group of integer modulo p i α i.

For the purpose of automorphism between two aligned DNA sequences,p i α i ∈ {5, 26, 53}.

Status

This application is currently available in Bioconductor (version 3.18)https://doi.org/doi:10.18129/B9.bioc.GenomAutomorphism. Watch this repo or check for updates.

Tutorials

There are several tutorials on how to use the package atGenomAutomorphismwebsite

• Get started-with GenomAutomorphism
• Analysis of Automorphisms on a DNA Multiple Sequence Alignment
• Analysis of Automorphisms on a MSA of Primate BRCA1 Gene
• A Short Introduction to Algebraic Taxonomy on Genes Regions
• Automorphism analysis on COVID-19 data
• Modular Matrix Operations of Mutational Events

Dependences

This package depends, so far, from: Biostrings, GenomicRanges,numbers, and S4Vectors.

Installation of R dependencies:

    if (!requireNamespace("BiocManager")) install.packages("BiocManager")

    BiocManager::install(c("Biostrings", "GenomicRanges", "S4Vectors",
    "BiocParallel", "GenomeInfoDb", "BiocGenerics", "numbers", "devtools",
    "doParallel", "data.table", "foreach","parallel"), dependencies = TRUE)

You can install GenomAutomorphism package from GitHub

   BiocManager::install('genomaths/GenomAutomorphism')

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. Sanchez R, Grau R, Morgado E. A novel Lie algebra of the genetic code over the Galois field of four DNA bases. Math Biosci. 2006;202: 156–174. doi:10.1016/j.mbs.2006.03.017
3. Sanchez R, Grau R. An algebraic hypothesis about the primeval genetic code architecture. Math Biosci. 2009/07/18. 2009;221: 60–76.doi:10.1016/j.mbs.2009.07.001
4. Robersy Sanchez, Jesús Barreto (2021) Genomic Abelian Finite Groups.doi: 10.1101/2021.06.01.446543.
5. M. V José, E.R. Morgado, R. Sánchez, 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.
6. 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.
7. Sanchez, R., 2014. Evolutionary Analysis of DNA-protein-coding regions based on a genetic code cube metric. Current Topics in Medicinal Chemistry, 14(3), pp.407-417. https://doi.org/10.2174/1568026613666131204110022.

See also

Symmetric Group of the Genetic-Code Cubes