consunsus_sequence: consunsus_sequence

In PSSMCOOL: Features Extracted from Position Specific Scoring Matrix (PSSM)

Description

This feature vector is constructed from PSSM Matrix as: α(i)=argmax(P_{i,j}) where i varies between 1 and L and j between 1 and 20, L indicates protein length and "arg" represents the argument of the maximum the ith base of the consensus sequence (CS) is then set to be the α(i)th amino acid in the amino acid alphabet and a consensus sequence is constructed.

Usage

consunsus_sequence(pssm_name)

Arguments

pssm_name

is the name of PSSM Matrix file

Value

consunsus sequence wich extracted from PSSM

References

Y. Liang, S. Liu, S. J. C. Zhang, and m. m. i. medicine, "Prediction of protein structural classes for low-similarity sequences based on consensus sequence and segmented PSSM," vol. 2015, 2015.

Examples

X<-consunsus_sequence(system.file("extdata", "C7GQS7.txt.pssm", package="PSSMCOOL"))

PSSMCOOL documentation built on Jan. 4, 2022, 5:07 p.m.