Skip to contents

List of 571 Amino Acid Physicochemical Indexes from AAindex Database

Source: R/data_aaindex1.R
aaindex1.Rd

The aminoacid indexes 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("aaindex1", package = "GenomAutomorphism")

Format

A list carrying the the description 566 Amino Acid Indices in AAindex ver.9.2 and the text file with the matrices imported from https://www.genome.jp/aaindex/.

See also

aaindex2 and aaindex3.

Author

Robersy Sanchez https://genomaths.com

Examples

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

## Get the available aminoacid indices.
mat <- aa_phychem_index(aaindex = "aaindex1", acc_list = TRUE)
mat[1:10]
#>  [1] "List of 566 Amino Acid Indices in AAindex ver.9.2"                            
#>  [2] ""                                                                             
#>  [3] "The columns correspond to the AAindex accession number and the description of"
#>  [4] "each index."                                                                  
#>  [5] ""                                                                             
#>  [6] "ANDN920101 alpha-CH chemical shifts (Andersen et al., 1992)"                  
#>  [7] "ARGP820101 Hydrophobicity index (Argos et al., 1982)"                         
#>  [8] "ARGP820102 Signal sequence helical potential (Argos et al., 1982)"            
#>  [9] "ARGP820103 Membrane-buried preference parameters (Argos et al., 1982)"        
#> [10] "BEGF750101 Conformational parameter of inner helix (Beghin-Dirkx, 1975)"