aaindex2: List of 94 Amino Acid Matrices from AAindex

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

List of 94 Amino Acid Matrices from AAindex

Description

The aminoacid similarity matrices from Amino Acid Index Database https://www.genome.jp/aaindex/ are provided here. AAindex (ver.9.2) is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids.

Usage

data("aaindex2", package = "GenomAutomorphism")

Format

A list carrying the description of 94 Amino Acid Matrices in AAindex ver.9.2 and the text file of matrices imported from https://www.genome.jp/aaindex/.

Details

The similarity of amino acids can be represented numerically, expressed in terms of observed mutation rate or physicochemical properties. A similarity matrix, also called a mutation matrix, is a set of 210 numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used for sequence alignments and similarity searches.

Author(s)

Robersy Sanchez https://genomaths.com

See Also

aaindex2 and aa_mutmat, and get_mutscore.

Examples

## Load the mutation matrices from database from the packages
data("aaindex2", package = "GenomAutomorphism")

## Get the available matrices
mat <- aa_mutmat(aaindex = "aaindex2", acc_list = TRUE)
mat[1:10]

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