aa_phychem_index: Amino acid mutation matrix

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

Amino acid mutation matrix

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.

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.

Function aa_phychem_index is wrapper function to call two other functions: aa_mutmat and aa_index

Usage

aa_phychem_index(acc = NA, aaindex = NA, acc_list = FALSE, info = FALSE)

aa_mutmat(acc = NA, aaindex = c("aaindex2", "aaindex3"), acc_list = FALSE)

aa_index(acc = NA, acc_list = FALSE, info = FALSE)

Arguments

acc	Accession id for a specified mutation or contact potential matrix.
aaindex	Database where the requested accession id is locate. The possible values are: "aaindex2" or "aaindex3".
acc_list	Logical. If TRUE, then the list of available matrices ids and index names is returned.
info	Logical. if TRUE, then whole information for the physicochemical index will be returned.

Value

Depending on the user specifications, a mutation or contact potential matrix, a list of available matrices (indices) ids or index names can be returned. More specifically:

aa_mutmat:

Returns an aminoacid mutation matrix or a statistical protein contact potentials matrix.

aa_index:

Returns the specified aminoacid physicochemical indices.

Author(s)

Robersy Sanchez https://genomaths.com

See Also

aaindex1, aaindex2, aaindex3, and get_mutscore.

Examples

## Load the mutation matrices from database from the packages
data("aaindex1","aaindex2", package = "GenomAutomorphism" )

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

## Return the 'Base-substitution-protein-stability matrix 
## (Miyazawa-Jernigan, 1993)'
aa_mutmat(acc = "MIYS930101", aaindex = "aaindex2")

## Return the 'BLOSUM80 substitution matrix (Henikoff-Henikoff, 1992)'
aa_mutmat(acc = "HENS920103", aaindex = "aaindex2")

## Using wrapping function
aa_phychem_index(acc = "EISD840101", aaindex = "aaindex1")

## Just the info. The information provided after the reference
## corresponds to the correlaiton of 'EISD840101' with other indices.
aa_phychem_index(acc = "EISD840101", aaindex = "aaindex1", info = TRUE)

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