This function calculates the normalized Moreau-Broto
autocorrelation descriptor (dim: length(props) * nlag
).
extractMoreauBroto(
x,
props = c("CIDH920105", "BHAR880101", "CHAM820101", "CHAM820102", "CHOC760101",
"BIGC670101", "CHAM810101", "DAYM780201"),
nlag = 30L,
customprops = NULL
)
A length length(props) * nlag
named vector.
A character vector, as the input protein sequence.
A character vector, specifying the Accession Number of the target properties. 8 properties are used by default, as listed below:
Normalized average hydrophobicity scales (Cid et al., 1992)
Average flexibility indices (Bhaskaran-Ponnuswamy, 1988)
Polarizability parameter (Charton-Charton, 1982)
Free energy of solution in water, kcal/mole (Charton-Charton, 1982)
Residue accessible surface area in tripeptide (Chothia, 1976)
Residue volume (Bigelow, 1967)
Steric parameter (Charton, 1981)
Relative mutability (Dayhoff et al., 1978b)
Maximum value of the lag parameter. Default is 30
.
A n x 21
named data frame contains n
customized property. Each row contains one property.
The column order for different amino acid types is
'AccNo'
, 'A'
, 'R'
, 'N'
,
'D'
, 'C'
, 'E'
, 'Q'
,
'G'
, 'H'
, 'I'
, 'L'
,
'K'
, 'M'
, 'F'
, 'P'
,
'S'
, 'T'
, 'W'
, 'Y'
,
'V'
, and the columns should also be exactly named like this.
The AccNo
column contains the properties' names.
Then users should explicitly specify these properties
with these names in the argument props
.
See the examples below for a demonstration.
The default value for customprops
is NULL
.
Nan Xiao <https://nanx.me>
AAindex: Amino acid index database. https://www.genome.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 extractMoran
and extractGeary
for Moran autocorrelation descriptors and Geary autocorrelation descriptors.
x <- readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]
extractMoreauBroto(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
extractMoreauBroto(
x,
customprops = myprops,
props = c(
"CIDH920105", "BHAR880101",
"CHAM820101", "CHAM820102",
"MyProp1", "MyProp2", "MyProp3"
)
)
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