R/414-extractProtAPAAC.R
extractProtAPAAC.Rd
Amphiphilic Pseudo Amino Acid Composition Descriptor
extractProtAPAAC(x, props = c("Hydrophobicity", "Hydrophilicity"), lambda = 30, w = 0.05, customprops = NULL)
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:
|
lambda | The lambda parameter for the APAAC descriptors, default is 30. |
w | The weighting factor, default is 0.05. |
customprops | A |
A length 20 + n * lambda
named vector,
n
is the number of properties selected.
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).
Note the default 20 * 2
prop
values have been already
independently given in the function. Users could also specify
other (up to 544) properties with the Accession Number in
the AAindex
data, with or without the default
three properties, which means users should explicitly specify
the properties to use.
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 extractProtPAAC
for pseudo
amino acid composition descriptor.
# NOT RUN { x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]] extractProtAPAAC(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 extractProtAPAAC(x, customprops = myprops, props = c('Hydrophobicity', 'Hydrophilicity', 'CIDH920105', 'BHAR880101', 'CHAM820101', 'CHAM820102', 'MyProp1', 'MyProp2', 'MyProp3')) # }