aa2index. bio3d 2.3-0

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).

Description

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

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.

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.

Examples

## 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 


## Use a sliding window average
aa2index(aa=seq, index=22, window=3)

   R    S    D    X    -    X    R    H    Q    V    L 
0.18 0.15 0.08 0.10  NaN 0.29 0.26 0.23 0.18 0.17 0.16 


## 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)) 

  BIGC670101 BULH740102 CHOC750101 COHE430101 FAUJ880103 GOLD730102 GRAR740103
R      77.47       0.63     141.87       0.66       3.50     126.90      70.00
S      77.47       0.63     141.87       0.66       3.50     126.90      70.00
D      77.47       0.63     141.87       0.66       3.50     126.90      70.00
X      61.65       0.58     111.80       0.64       2.19      99.75      43.00
-      88.75       0.64     163.25       0.65       4.46     146.00      89.00
X     100.50       0.69     184.65       0.68       5.39     166.90     110.00
R      96.90       0.67     176.80       0.68       4.91     160.83     101.67
H      93.95       0.70     168.03       0.72       4.44     155.97      97.25
Q      95.56       0.73     168.00       0.76       4.35     158.48     100.00
V      92.17       0.73     159.50       0.78       3.90     152.80      94.00
L      92.27       0.76     156.90       0.81       3.65     152.87      93.33
  KRIW790103 TSAJ990101 TSAJ990102 HARY940101 PONJ960101
R      58.10     132.97     135.57     134.70     144.43
S      58.10     132.97     135.57     134.70     144.43
D      58.10     132.97     135.57     134.70     144.43
X      34.65     104.30     106.35     105.65     118.60
-      72.50     152.35     155.65     154.95     165.65
X      92.00     173.90     177.00     176.05     179.65
R      88.23     164.90     167.80     167.17     171.90
H      84.05     158.22     160.60     160.15     163.53
Q      85.94     159.20     161.28     161.04     163.50
V      81.17     151.43     153.10     153.10     155.35
L      81.90     149.40     150.80     151.03     152.73

Author

Ana Rodrigues

Convert an Aminoacid Sequence to AAIndex Values