mut_type: Classification of DNA base mutations

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

Classification of DNA base mutations

Description

Each DNA/RNA base can be classified into three main classes according to three criteria (1): number of hydrogen bonds (strong-weak), chemical type (purine-pyrimidine), and chemical groups (amino versus keto). Each criterion produces a partition of the set of bases: 1) According to the number of hydrogen bonds (on DNA/RNA double helix): strong S=(C,G) (three hydrogen bonds) and weak W=(A,U) (two hydrogen bonds). According to the chemical type: purines R=(A, G) and pyrimidines Y=(C,U). 3). According to the presence of amino or keto groups on the base rings: amino M=(C,A) and keto K=(G,U). So, each mutational event can be classified as according to the type of involved in it (2).

Usage

mut_type(x, y)

Arguments

x, y	Character strings denoting DNA bases

Value

A character string of same length of 'x' and 'y'.

References

1. A. Cornish-Bowden, Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984, Nucleic Acids Res. 13 (1985) 3021-3030.

2. MA.A. Jimenez-Montano, C.R. de la Mora-Basanez, T. Poschel, The hypercube structure of the genetic code explains conservative and non-conservative aminoacid substitutions in vivo and in vitro, Biosystems. 39 (1996) 117-125.

Examples

## Mutation type 'R'
mut_type("A", "G")

## Mutation type 'M'
mut_type("A", "C")

## Mutation type 'W'
mut_type("A", "T")

## Mutation type 'S'
mut_type("G", "C")

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