bio3d (version 2.3-4)

aa2index: Convert an Aminoacid Sequence to AAIndex Values

Description

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

Usage

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

Arguments

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).

Value

Returns a numeric vector.

Details

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.

References

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: http://www.genome.jp/aaindex/ or the aa.index documentation.

See Also

aa.index, read.fasta

Examples

# NOT RUN {
## 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)) 
# }