extractQSO: Quasi-Sequence-Order (QSO) Descriptor

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/desc-12-QSO.R

Description

This function calculates the Quasi-Sequence-Order (QSO) descriptor (dim: 20 + 20 + (2 * nlag), default is 100).

Usage

1
extractQSO(x, nlag = 30, w = 0.1)

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.

Value

A length 20 + 20 + (2 * nlag) named vector

Author(s)

Nan Xiao <https://nanx.me>

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.

Examples

1
2
x = readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]
extractQSO(x)

Example output

 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 

protr documentation built on Feb. 25, 2019, 1:04 a.m.