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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](https://www.biorxiv.org/content/10.1101/2021.06.01.446543v2)

https://github.com/genomaths/genomautomorphism

Science Score: 46.0%

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    Found 12 DOI reference(s) in README
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    Links to: arxiv.org, biorxiv.org
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Keywords

genetic-code genetic-code-algebra genome genome-algebra
Last synced: 9 months ago · JSON representation

Repository

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](https://www.biorxiv.org/content/10.1101/2021.06.01.446543v2)

Basic Info
  • Host: GitHub
  • Owner: genomaths
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 2.07 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
genetic-code genetic-code-algebra genome genome-algebra
Created over 4 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog

README.md

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 = (ℤp1α1)n1 ⊕ (ℤp1α2)n2 ⊕ … ⊕ (ℤpkαk)nk

Where, the pi’s are prime numbers, αi ∈ ℕ and ℤpiαi is the group of integer modulo piαi.

For the purpose of automorphism between two aligned DNA sequences, piαi ∈ {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 website

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

Owner

  • Name: Robersy Sanchez
  • Login: genomaths
  • Kind: user
  • Location: State College
  • Company: Penn State

Mathematical Biologist

GitHub Events

Total
  • Push event: 2
Last Year
  • Push event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 114
  • Total Committers: 3
  • Avg Commits per committer: 38.0
  • Development Distribution Score (DDS): 0.237
Past Year
  • Commits: 13
  • Committers: 2
  • Avg Commits per committer: 6.5
  • Development Distribution Score (DDS): 0.077
Top Committers
Name Email Commits
genomaths 1****s 87
Robersy Sanchez r****7@p****u 26
J Wokaty j****y@s****u 1
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1 psu.edu: 1

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Last synced: 10 months ago

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  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
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Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 5,577 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: GenomAutomorphism

Compute the automorphisms between DNA's Abelian group representations

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 5,577 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 19.8%
Average: 29.5%
Stargazers count: 33.2%
Downloads: 94.8%
Maintainers (1)
genomicmath@gmail.com
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.2 depends
  • BiocGenerics * imports
  • BiocParallel * imports
  • Biostrings * imports
  • GenomeInfoDb * imports
  • GenomicRanges * imports
  • IRanges * imports
  • S4Vectors * imports
  • data.table * imports
  • doParallel * imports
  • dplyr * imports
  • foreach * imports
  • methods * imports
  • numbers * imports
  • parallel * imports
  • stats * imports
  • BiocStyle * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • spelling * suggests
  • testthat >= 3.0.0 suggests