This function calculates the Quasi-Sequence-Order (QSO) descriptor
(dim: 20 + 20 + (2 * nlag), default is 100).
Arguments
- x
A character vector, as the input protein sequence.
- nlag
The maximum lag, defualt is 30.
- w
The weighting factor, default is 0.1.
References
Kuo-Chen Chou. Prediction of Protein Subcellar Locations by Incorporating Quasi-Sequence-Order Effect. Biochemical and Biophysical Research Communications, 2000, 278, 477-483.
Kuo-Chen Chou and Yu-Dong Cai. Prediction of Protein Sucellular Locations by GO-FunD-PseAA Predictor. Biochemical and Biophysical Research Communications, 2004, 320, 1236-1239.
Gisbert Schneider and Paul Wrede. The Rational Design of Amino Acid Sequences by Artifical Neural Networks and Simulated Molecular Evolution: Do Novo Design of an Idealized Leader Cleavge Site. Biophys Journal, 1994, 66, 335-344.
See also
See extractSOCN for sequence-order-coupling numbers.
Author
Nan Xiao <https://nanx.me>
Examples
x <- readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]
extractQSO(x)
#> Schneider.Xr.A Schneider.Xr.R Schneider.Xr.N Schneider.Xr.D Schneider.Xr.C
#> 6.096218e-02 6.773576e-02 3.725467e-02 4.910842e-02 6.434897e-02
#> Schneider.Xr.E Schneider.Xr.Q Schneider.Xr.G Schneider.Xr.H Schneider.Xr.I
#> 4.572164e-02 4.572164e-02 7.789612e-02 2.878770e-02 3.386788e-02
#> Schneider.Xr.L Schneider.Xr.K Schneider.Xr.M Schneider.Xr.F Schneider.Xr.P
#> 7.281594e-02 3.725467e-02 1.185376e-02 3.048109e-02 5.080182e-02
#> Schneider.Xr.S Schneider.Xr.T Schneider.Xr.W Schneider.Xr.Y Schneider.Xr.V
#> 8.466970e-02 4.233485e-02 2.201412e-02 4.064145e-02 4.741503e-02
#> Grantham.Xr.A Grantham.Xr.R Grantham.Xr.N Grantham.Xr.D Grantham.Xr.C
#> 1.835033e-06 2.038926e-06 1.121409e-06 1.478221e-06 1.936980e-06
#> Grantham.Xr.E Grantham.Xr.Q Grantham.Xr.G Grantham.Xr.H Grantham.Xr.I
#> 1.376275e-06 1.376275e-06 2.344765e-06 8.665435e-07 1.019463e-06
#> Grantham.Xr.L Grantham.Xr.K Grantham.Xr.M Grantham.Xr.F Grantham.Xr.P
#> 2.191845e-06 1.121409e-06 3.568120e-07 9.175167e-07 1.529194e-06
#> Grantham.Xr.S Grantham.Xr.T Grantham.Xr.W Grantham.Xr.Y Grantham.Xr.V
#> 2.548657e-06 1.274329e-06 6.626509e-07 1.223356e-06 1.427248e-06
#> Schneider.Xd.1 Schneider.Xd.2 Schneider.Xd.3 Schneider.Xd.4 Schneider.Xd.5
#> 3.457972e-02 3.384600e-02 3.502111e-02 3.344162e-02 3.273951e-02
#> Schneider.Xd.6 Schneider.Xd.7 Schneider.Xd.8 Schneider.Xd.9 Schneider.Xd.10
#> 3.525537e-02 3.311390e-02 3.403364e-02 3.331093e-02 3.285068e-02
#> Schneider.Xd.11 Schneider.Xd.12 Schneider.Xd.13 Schneider.Xd.14 Schneider.Xd.15
#> 3.381760e-02 3.470422e-02 3.166883e-02 3.360882e-02 3.479121e-02
#> Schneider.Xd.16 Schneider.Xd.17 Schneider.Xd.18 Schneider.Xd.19 Schneider.Xd.20
#> 3.270408e-02 3.172623e-02 3.225829e-02 3.435647e-02 3.361893e-02
#> Schneider.Xd.21 Schneider.Xd.22 Schneider.Xd.23 Schneider.Xd.24 Schneider.Xd.25
#> 3.236099e-02 3.132904e-02 3.217206e-02 3.432701e-02 3.414334e-02
#> Schneider.Xd.26 Schneider.Xd.27 Schneider.Xd.28 Schneider.Xd.29 Schneider.Xd.30
#> 3.294954e-02 3.149609e-02 3.456720e-02 3.237140e-02 3.114275e-02
#> Grantham.Xd.1 Grantham.Xd.2 Grantham.Xd.3 Grantham.Xd.4 Grantham.Xd.5
#> 3.402298e-02 3.446605e-02 3.638918e-02 3.439801e-02 3.206838e-02
#> Grantham.Xd.6 Grantham.Xd.7 Grantham.Xd.8 Grantham.Xd.9 Grantham.Xd.10
#> 3.486488e-02 3.361253e-02 3.341875e-02 3.374516e-02 3.451195e-02
#> Grantham.Xd.11 Grantham.Xd.12 Grantham.Xd.13 Grantham.Xd.14 Grantham.Xd.15
#> 3.311057e-02 3.499580e-02 3.209915e-02 3.312361e-02 3.372162e-02
#> Grantham.Xd.16 Grantham.Xd.17 Grantham.Xd.18 Grantham.Xd.19 Grantham.Xd.20
#> 3.350302e-02 3.348467e-02 3.147055e-02 3.349358e-02 3.298629e-02
#> Grantham.Xd.21 Grantham.Xd.22 Grantham.Xd.23 Grantham.Xd.24 Grantham.Xd.25
#> 3.293706e-02 3.027516e-02 3.329628e-02 3.390974e-02 3.303396e-02
#> Grantham.Xd.26 Grantham.Xd.27 Grantham.Xd.28 Grantham.Xd.29 Grantham.Xd.30
#> 3.253250e-02 3.199340e-02 3.332438e-02 3.284195e-02 3.236875e-02