pssm_ac: auto covariance transformation feature vector

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

Description

The AC variable measures the correlation of the same property between two residues separated by a distance of lg along the sequence

Usage

pssm_ac(pssm_name, lg = 10)

Arguments

pssm_name	name of the PSSM Matrix file
lg	a parameter which indicates distance between two residues

Value

feature vector which its length depends on parameter lg. by default lg is 10 hence feature vector would be of length 200.

Note

in use of this function The lg parameter must be less than the length of the smallest sequence in the database.

References

Dong, Q., Zhou, S. and Guan, J. (2009) A new taxonomy-based protein fold recognition approach based on autocross-covariance transformation, Bioinformatics, 25, 2655-2662.

Examples

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

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