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<!-- is generated from README.Rmd. Please edit that file --> # GenomAutomorphism [<img src="man/figures/logo.png" align="right" />]( Robersy Sanchez Department of Biology. Eberly College of Science. Pennsylvania State University, University Park, PA 16802 <> [ORCID:]( ## 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<sub>*p*<sub>1</sub><sup>*α*<sub>1</sub></sup></sub>)<sup>*n*<sub>1</sub></sup> ⊕ (ℤ<sub>*p*<sub>1</sub><sup>*α*<sub>2</sub></sup></sub>)<sup>*n*<sub>2</sub></sup> ⊕ … ⊕ (ℤ<sub>*p*<sub>*k*</sub><sup>*α*<sub>*k*</sub></sup></sub>)<sup>*n*<sub>*k*</sub></sup> Where, the *p*<sub>*i*</sub>’s are prime numbers, *α*<sub>*i*</sub> ∈ ℕ and ℤ<sub>*p*<sub>*i*</sub><sup>*α*<sub>*i*</sub></sup></sub> is the group of integer modulo *p*<sub>*i*</sub><sup>*α*<sub>*i*</sub></sup>. For the purpose of automorphism between two aligned DNA sequences, *p*<sub>*i*</sub><sup>*α*<sub>*i*</sub></sup> ∈ {5, 2<sup>6</sup>, 5<sup>3</sup>}. ------------------------------------------------------------------------ ## Status This application is currently available in Bioconductor (version 3.18) <>. Watch this repo or check for updates. ------------------------------------------------------------------------ ## Tutorials There are several tutorials on how to use the package at [GenomAutomorphism]( website [<img src="man/figures/logo.png" align="middle" width="32" height="32" />]( - <a href="" target="_blank" rel="noopener">Get started-with GenomAutomorphism</a> - <a href="" target="_blank" rel="noopener">Analysis of Automorphisms on a DNA Multiple Sequence Alignment</a> - <a href="" target="_blank" rel="noopener">Analysis of Automorphisms on a MSA of Primate BRCA1 Gene</a> - <a href="" target="_blank" rel="noopener">A Short Introduction to Algebraic Taxonomy on Genes Regions</a> - <a href="" target="_blank" rel="noopener">Automorphism analysis on COVID-19 data</a> - <a href="" 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]( 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. ## See also [Symmetric Group of the Genetic-Code Cubes](