aaindex2 | R Documentation |
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.
data("aaindex2", package = "GenomAutomorphism")
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/.
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.
Robersy Sanchez https://genomaths.com
aaindex2
and aa_mutmat
, and
get_mutscore
.
## 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]
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