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Detecting Amino Acid Coevolution with Bayesian Graphical Models

  • Mariano Avino
  • Art F. Y. Poon
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1851)

Abstract

The comparative study of homologous proteins can provide abundant information about the functional and structural constraints on protein evolution. For example, an amino acid substitution that is deleterious may become permissive in the presence of another substitution at a second site of the protein. A popular approach for detecting coevolving residues is by looking for correlated substitution events on branches of the molecular phylogeny relating the protein-coding sequences. Here we describe a machine learning method (Bayesian graphical models) implemented in the open-source phylogenetic software package HyPhy, http://hyphy.org, for extracting a network of coevolving residues from a sequence alignment.

Key words

amino acid coevolution Bayesian graphical model hepatitis C virus HyPhy epistasis 

Notes

Acknowledgements

This study was supported in part by the Government of Canada through Genome Canada and the Ontario Genomics Institute (OGI-131), and by grants from the Canadian Institutes of Health Research (PJT-153391 and BOP-149562). AFYP was supported by a CIHR New Investigator Award (FRN-130609).

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Pathology and Laboratory MedicineWestern UniversityLondonCanada

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