Converts sequences to aminoacid indeces from the ‘AAindex’ database.

aa2index(aa, index = "KYTJ820101", window = 1)



a protein sequence character vector.


an index name or number (default: “KYTJ820101”, hydropathy index by Kyte-Doolittle, 1982).


a positive numeric value, indicating the window size for smoothing with a sliding window average (default: 1, i.e. no smoothing).


By default, this function simply returns the index values for each amino acid in the sequence. It can also be set to perform a crude sliding window average through the window argument.


Returns a numeric vector.


Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

‘AAIndex’ is the work of Kanehisa and co-workers: Kawashima and Kanehisa (2000) Nucleic Acids Res. 28, 374; Tomii and Kanehisa (1996) Protein Eng. 9, 27--36; Nakai, Kidera and Kanehisa (1988) Protein Eng. 2, 93--100.

For a description of the ‘AAindex’ database see: or the aa.index documentation.


Ana Rodrigues

See also


## Residue hydropathy values seq <- c("R","S","D","X","-","X","R","H","Q","V","L") aa2index(seq)
#> R S D <NA> <NA> <NA> R H Q V L #> -4.5 -0.8 -3.5 NA NA NA -4.5 -3.2 -3.5 4.2 3.8
if (FALSE) { ## Use a sliding window average aa2index(aa=seq, index=22, window=3) ## Use an alignment aln <- read.fasta(system.file("examples/hivp_xray.fa",package="bio3d")) prop <- t(apply(aln$ali, 1, aa2index, window=1)) ## find and use indices for volume calculations i <- which(sapply(aa.index, function(x) length(grep("volume", x$D, != 0)) sapply(i, function(x) aa2index(aa=seq, index=x, window=5)) }