A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins

AUTOR(ES)

Knudsen, Bjarne

FONTE

The National Academy of Sciences

RESUMO

Changes in protein function can lead to changes in the selection acting on specific residues. This can often be detected as evolutionary rate changes at the sites in question. A maximum-likelihood method for detecting evolutionary rate shifts at specific protein positions is presented. The method determines significance values of the rate differences to give a sound statistical foundation for the conclusions drawn from the analyses. A statistical test for detecting slowly evolving sites is also described. The methods are applied to a set of Myc proteins for the identification of both conserved sites and those with changing evolutionary rates. Those positions with conserved and changing rates are related to the structures and functions of their proteins. The results are compared with an earlier Bayesian method, thereby highlighting the advantages of the new likelihood ratio tests.

Documentos Relacionados

• Severe Acute Respiratory Syndrome Coronavirus Sequence Characteristics and Evolutionary Rate Estimate from Maximum Likelihood Analysis
• Relationship between evolutionary rate and cellular location among the Inv/Spa invasion proteins of Salmonella enterica.
• Annotation Transfer for Genomics: Measuring Functional Divergence in Multi-Domain Proteins
• Domain mobility in proteins: functional and evolutionary implications
• Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins