R: Convert an Aminoacid Sequence to AAIndex Values

aa2index {bio3d} | R Documentation

## 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).

### 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.

### Value

Returns a numeric vector.

### Author(s)

Ana Rodrigues

### 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

    ## 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))

    ## End(Not run)

[Package bio3d version 2.3-3 Index]