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aaSEA (version 1.1.0)

Amino Acid Substitution Effect Analyser

Description

Given a protein multiple sequence alignment, it is daunting task to assess the effects of substitutions along sequence length. 'aaSEA' package is intended to help researchers to rapidly analyse property changes caused by single, multiple and correlated amino acid substitutions in proteins. Methods for identification of co-evolving positions from multiple sequence alignment are as described in : Pel et al., (2017) .

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Version

Install

install.packages('aaSEA')

Monthly Downloads

23

Version

1.1.0

License

GPL-3

Maintainer

Raja Reddy D.M

Last Published

November 9th, 2019

Functions in aaSEA (1.1.0)

Get correlated sites with substitutions

getCorPropChange

Get property changes associated with correlated substitutions

A data frame of 10 Kidera factors for 20 amino acids

plotSingleSubChange

Plots single substitution change histogram

A data frame of six Fasgai vectors for 20 amino acids.

plotMultiSubChange

Plots heat map of multiple substitution associated changes per site

Get wild type and substituted amino acid properties and associated property changes

Title Enables to start and run the app

A data frame of 3 Cruciani properties for 20 amino acids.

Get amino acid property wise correlations of co-evolving columns of a multiple sequence alignment

Get amino acid substitutions from multiple sequence alignment

Get sites with more than one-correlated substitutions other than conserved amino acids at that position

Function to encode Correlated columns of alignment matrix with desired properties

simple interactive network diagram of correlated substitution pairs

plotCorSubChanges

Plot co-evolving sites with selected property correlations

A data frame of correlated sites.

A data frame of 533 amino acid properties from AAindex.