protr (version 0.3-1)

extractAPAAC: Amphiphilic Pseudo Amino Acid Composition Descriptor

Description

Amphiphilic Pseudo Amino Acid Composition Descriptor

Usage

extractAPAAC(x, props = c("Hydrophobicity", "Hydrophilicity"), lambda = 30,
  w = 0.05, customprops = NULL)

Arguments

x

A character vector, as the input protein sequence.

props

A character vector, specifying the properties used. 2 properties are used by default, as listed below: [object Object],[object Object]

lambda

The lambda parameter for the APAAC descriptors, default is 30.

w

The weighting factor, default is 0.05.

customprops

A n x 21 named data frame contains n customize property. Each row contains one property. The column order for different amino acid types is 'AccNo', 'A', 'R', 'N', 'D

Value

• A length 20 + n * lambda named vector, n is the number of properties selected.

Details

This function calculates the Amphiphilic Pseudo Amino Acid Composition (APAAC) descriptor (Dim: 20 + (n * lambda), n is the number of properties selected, default is 80).

References

Kuo-Chen Chou. Prediction of Protein Cellular Attributes Using Pseudo-Amino Acid Composition. PROTEINS: Structure, Function, and Genetics, 2001, 43: 246-255.

Type 2 pseudo amino acid composition. http://www.csbio.sjtu.edu.cn/bioinf/PseAAC/type2.htm

Kuo-Chen Chou. Using Amphiphilic Pseudo Amino Acid Composition to Predict Enzyme Subfamily Classes. Bioinformatics, 2005, 21, 10-19.

JACS, 1962, 84: 4240-4246. (C. Tanford). (The hydrophobicity data)

PNAS, 1981, 78:3824-3828 (T.P.Hopp & K.R.Woods). (The hydrophilicity data)

See Also

See extractPAAC for pseudo amino acid composition descriptor.

Examples

x = readFASTA(system.file('protseq/P00750.fasta', package = 'protr'))[[1]]
extractAPAAC(x)

myprops = data.frame(AccNo = c("MyProp1", "MyProp2", "MyProp3"),
                     A = c(0.62,  -0.5, 15),  R = c(-2.53,   3, 101),
                     N = c(-0.78,  0.2, 58),  D = c(-0.9,    3, 59),
                     C = c(0.29,    -1, 47),  E = c(-0.74,   3, 73),
                     Q = c(-0.85,  0.2, 72),  G = c(0.48,    0, 1),
                     H = c(-0.4,  -0.5, 82),  I = c(1.38, -1.8, 57),
                     L = c(1.06,  -1.8, 57),  K = c(-1.5,    3, 73),
                     M = c(0.64,  -1.3, 75),  F = c(1.19, -2.5, 91),
                     P = c(0.12,     0, 42),  S = c(-0.18, 0.3, 31),
                     T = c(-0.05, -0.4, 45),  W = c(0.81, -3.4, 130),
                     Y = c(0.26,  -2.3, 107), V = c(1.08, -1.5, 43))

# Use 2 default properties, 4 properties in the AAindex database,
# and 3 cutomized properties
extractAPAAC(x, customprops = myprops,
             props = c('Hydrophobicity', 'Hydrophilicity',
                       'CIDH920105', 'BHAR880101',
                       'CHAM820101', 'CHAM820102',
                       'MyProp1', 'MyProp2', 'MyProp3'))