Bios2cor:From Biological Sequences and Simulations to Correlation
Analysis
Utilities for computation and analysis of correlation/covariation in multiple sequence alignments and in
side chain motions during molecular dynamics simulations.
Features include the computation of correlation/covariation
scores using a variety of scoring functions between either
sequence positions in alignments or side chain dihedral angles
in molecular dynamics simulations and utilities to analyze the
correlation/covariation matrix through a variety of tools
including network representation and principal components
analysis. In addition, several utility functions are based on
the R graphical environment to provide friendly tools for help
in data interpretation. Examples of sequence covariation
analysis are provided in: (1) Pele J, Moreau M, Abdi H, Rodien
P, Castel H, Chabbert M (2014) <doi:10.1002/prot.24570> and (2)
Taddese B, Deniaud M, Garnier A, Tiss A, Guissouma H, Abdi H,
Henrion D, Chabbert M (2018)
<doi:10.1371/journal.pcbi.1006209>. An example of side chain
correlated motion analysis is provided in: Taddese B, Garnier
A, Abdi H, Henrion D, Chabbert M (2020)
<doi:10.1038/s41598-020-72766-1>. This work was supported by
the French National Research Agency (Grant number:
ANR-11-BSV2-026) and by GENCI (Grant number: 100567).
