R/404-extractProtMoreauBroto.R
extractProtMoreauBroto.Rd
Normalized Moreau-Broto Autocorrelation Descriptor
extractProtMoreauBroto(x, props = c("CIDH920105", "BHAR880101", "CHAM820101", "CHAM820102", "CHOC760101", "BIGC670101", "CHAM810101", "DAYM780201"), nlag = 30L, customprops = NULL)
x | A character vector, as the input protein sequence. |
---|---|
props | A character vector, specifying the Accession Number of the target properties. 8 properties are used by default, as listed below:
|
nlag | Maximum value of the lag parameter. Default is |
customprops | A |
A length nlag
named vector
This function calculates the normalized Moreau-Broto
autocorrelation descriptor (Dim: length(props) * nlag
).
AAindex: Amino acid index database. http://www.genome.ad.jp/dbget/aaindex.html
Feng, Z.P. and Zhang, C.T. (2000) Prediction of membrane protein types based on the hydrophobic index of amino acids. Journal of Protein Chemistry, 19, 269-275.
Horne, D.S. (1988) Prediction of protein helix content from an autocorrelation analysis of sequence hydrophobicities. Biopolymers, 27, 451-477.
Sokal, R.R. and Thomson, B.A. (2006) Population structure inferred by local spatial autocorrelation: an usage from an Amerindian tribal population. American Journal of Physical Anthropology, 129, 121-131.
See extractProtMoran
and extractProtGeary
for Moran autocorrelation descriptors and
Geary autocorrelation descriptors.
# NOT RUN { x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]] extractProtMoreauBroto(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 4 properties in the AAindex database, and 3 cutomized properties extractProtMoreauBroto(x, customprops = myprops, props = c('CIDH920105', 'BHAR880101', 'CHAM820101', 'CHAM820102', 'MyProp1', 'MyProp2', 'MyProp3')) # }