blosumIndices: Compute the BLOSUM62 derived indices of a protein sequence

In Peptides: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences

Compute the BLOSUM62 derived indices of a protein sequence

Description

BLOSUM indices were derived of physicochemical properties that have been subjected to a VARIMAX analyses and an alignment matrix of the 20 natural AAs using the BLOSUM62 matrix.

Usage

blosumIndices(seq)

Arguments

seq	An amino-acids sequence

Value

The computed average of BLOSUM indices of all the amino acids in the corresponding peptide sequence.

References

Georgiev, A. G. (2009). Interpretable numerical descriptors of amino acid space. Journal of Computational Biology, 16(5), 703-723.

Examples

blosumIndices(seq = "KLKLLLLLKLK")
# [[1]]
#   BLOSUM1    BLOSUM2    BLOSUM3    BLOSUM4    BLOSUM5    
# -0.4827273 -0.5618182 -0.8509091 -0.4172727  0.3172727  

#  BLOSUM6   BLOSUM7     BLOSUM8    BLOSUM9   BLOSUM10 
# 0.2527273  0.1463636  0.1427273 -0.2145455 -0.3218182 

Peptides documentation built on May 29, 2024, 11:02 a.m.