Convert an Aminoacid Sequence to AAIndex Values
Converts sequences to aminoacid indeces from the ‘AAindex’ database.
aa2index(aa, index = "KYTJ820101", window = 1)
aa |
a protein sequence character vector. |
index |
an index name or number (default: “KYTJ820101”, hydropathy index by Kyte-Doolittle, 1982). |
window |
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.
Ana Rodrigues
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:
https://www.genome.jp/aaindex/ or the aa.index documentation.
## Residue hydropathy values
seq <- c("R","S","D","X","-","X","R","H","Q","V","L")
aa2index(seq)
## Not run:
## 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, ignore.case=TRUE)) != 0))
sapply(i, function(x) aa2index(aa=seq, index=x, window=5))
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