peplib (version 1.5.1)

blosum62: BLOSUM 62 substitution matrix

Description

The BLOSUM 62 substitution matrix which may be used for calculating distances. This is the default

Usage

data(blosum62)

Format

A matrix where element i,j represents how often homologous proteins have element i substituted with element j. Thus, it is a measure of similarity. Positive numbers indicate easy substitution, while negative numbers indicate difficult substitution.

Source

Henikoff, S.; Henikoff, J.G. (1992). "Amino Acid Substitution Matrices from Protein Blocks". PNAS 89 (22): 10915-10919. doi:10.1073/pnas.89.22.10915

Examples

data(blosum62)
##Change the normal distance parameters
default.MetricParams <-  new("MetricParams", smatrix=blosum62, gapOpen=-10, gapExtension=-0.2)
##Now calls to dist on sequences will use blosum 62 instead