Work

Measuring evolutionary rates of proteins in a structural context

Year: 2017

Type: article

Abstract: We describe how to measure site-specific rates of evolution in protein-coding genes and how to correlate these rates with structural features of the expressed protein, such as relative solvent accessibility, secondary structure, or weighted contact number. We present two alternative approaches to rate calculations: One based on relative amino-acid rates, and the other based on site-specific codon rates measured as dN / dS . We additionally provide a code repository containing scripts to facilitate the specific analysis protocols we recommend.

Source: F1000Research

DOI: 10.12688/f1000research.12874.1

Authors: Dariya K. Sydykova, Benjamin R. Jack, Stephanie J. Spielman, Claus O. Wilke

Institutions: The University of Texas at Austin, Temple University

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $1,350

Funders: National Science Foundation, National Institutes of Health, National Institute of General Medical Sciences, Army Research Office