<!-- README.md is generated from README.Rmd. Please edit that file --> # GenomAutomorphism [<img src="man/figures/logo.png" align="right" />](https://genomaths.github.io/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](https://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](https://www.biorxiv.org/content/10.1101/2021.06.01.446543v2). 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 at [GenomAutomorphism](https://genomaths.github.io/genomautomorphism) website [<img src="man/figures/logo.png" align="middle" width="32" height="32" />](https://genomaths.github.io/genomautomorphism) - <a href="https://is.gd/zwRaUw" target="_blank" rel="noopener">Get started-with GenomAutomorphism</a> - <a href="https://is.gd/A03Fkl" target="_blank" rel="noopener">Analysis of Automorphisms on a DNA Multiple Sequence Alignment</a> - <a href="https://is.gd/gsZcuj" target="_blank" rel="noopener">Analysis of Automorphisms on a MSA of Primate BRCA1 Gene</a> - <a href="https://is.gd/87wlbL" target="_blank" rel="noopener">A Short Introduction to Algebraic Taxonomy on Genes Regions</a> - <a href="https://is.gd/836uas" target="_blank" rel="noopener">Automorphism analysis on COVID-19 data</a> - <a href="https://is.gd/wlyzhr" target="_blank" rel="noopener">Modular Matrix Operations of Mutational Events</a> ## 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](https://arxiv.org/pdf/q-bio/0412033.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](https://doi.org/10.1016/j.mbs.2009.07.001) 4. Robersy Sanchez, Jesús Barreto (2021) Genomic Abelian Finite Groups. [doi: 10.1101/2021.06.01.446543](https://doi.org/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](https://is.gd/na9eap). 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](https://bit.ly/2Z9mjM7). 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](https://github.com/genomaths/GenomeAlgebra_SymmetricGroup)