QuasiSequenceOrder | index /home/orient/ProPy/propy/QuasiSequenceOrder.py

`##############################################################################################
This module is used for computing the quasi sequence order descriptors based on the
given protein sequence. We can obtain two types of descriptors: Sequence-order-coupling
number and quasi-sequence-order descriptors. Two distance matrixes between 20 amino acids
are employed. You can freely use and distribute it. If you have any problem, please contact
us immediately.
References:
[1]:Kuo-Chen Chou. Prediction of Protein Subcellar Locations by Incorporating
Quasi-Sequence-Order Effect. Biochemical and Biophysical Research Communications
2000, 278, 477-483.
[2]: 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.
[3]: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.
Authors: Dongsheng Cao and Yizeng Liang.
Date: 2012.09.03
Email: oriental-cds@163.com
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Modules
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math | string |  |

Functions
`` |  | GetAAComposition(ProteinSequence) `############################################################################### Calculate the composition of Amino acids for a given protein sequence. Usage: result=CalculateAAComposition(protein) Input: protein is a pure protein sequence. Output: result is a dict form containing the composition of 20 amino acids. ###############################################################################` GetQuasiSequenceOrder(ProteinSequence, maxlag=30, weight=0.1) `############################################################################### Computing quasi-sequence-order descriptors for a given protein. [1]:Kuo-Chen Chou. Prediction of Protein Subcellar Locations by Incorporating Quasi-Sequence-Order Effect. Biochemical and Biophysical Research Communications 2000, 278, 477-483. Usage: result = GetQuasiSequenceOrder(protein,maxlag,weight) Input: protein is a pure protein sequence maxlag is the maximum lag and the length of the protein should be larger than maxlag. default is 30. weight is a weight factor. please see reference 1 for its choice. Output: result is a dict form containing all quasi-sequence-order descriptors ###############################################################################` GetQuasiSequenceOrder1(ProteinSequence, maxlag=30, weight=0.1) `############################################################################### Computing the first 20 quasi-sequence-order descriptors for a given protein sequence. Usage: result = GetQuasiSequenceOrder1(protein,maxlag,weigt) see method GetQuasiSequenceOrder for the choice of parameters. ###############################################################################` GetQuasiSequenceOrder2(ProteinSequence, maxlag=30, weight=0.1) `############################################################################### Computing the last maxlag quasi-sequence-order descriptors for a given protein sequence. Usage: result = GetQuasiSequenceOrder2(protein,maxlag,weigt) see method GetQuasiSequenceOrder for the choice of parameters. ###############################################################################` GetSequenceOrderCouplingNumber(ProteinSequence, d=1) `############################################################################### Computing the dth-rank sequence order coupling number for a protein. Usage: result = GetSequenceOrderCouplingNumber(protein,d) Input: protein is a pure protein sequence. d is the gap between two amino acids. Output: result is numeric value. ###############################################################################` GetSequenceOrderCouplingNumberTotal(ProteinSequence, maxlag=30) `############################################################################### Computing the sequence order coupling numbers from 1 to maxlag for a given protein sequence. Usage: result = GetSequenceOrderCouplingNumberTotal(protein, maxlag) Input: protein is a pure protein sequence maxlag is the maximum lag and the length of the protein should be larger than maxlag. default is 30. Output: result is a dict form containing all sequence order coupling numbers ###############################################################################`

Data
`` |  | AALetter = ['A', 'R', 'N', 'D', 'C', 'E', 'Q', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V']