extrProtQSO: Quasi-Sequence-Order (QSO) Descriptor

In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

Description

Quasi-Sequence-Order (QSO) Descriptor

Usage

extrProtQSO(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.

Details

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

Value

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

Author(s)

Min-feng Zhu <[e-mail]>, Nan Xiao <http://r2s.name>

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 extrProtSOCN for sequence-order-coupling numbers.

Examples

x = readFASTA(system.file('protseq/P00750.fasta', package = 'BioMedR'))[[1]]
extrProtQSO(x)

BioMedR documentation built on Nov. 17, 2017, 10:08 a.m.