extractQSO: Quasi-Sequence-Order (QSO) Descriptor

In protr: Generating Various Numerical Representation Schemes for Protein Sequences

Quasi-Sequence-Order (QSO) Descriptor

Description

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

Usage

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

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

protr documentation built on Sept. 12, 2024, 6:44 a.m.