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Measuring codon usage bias

Alexander Roth, Maria Anisimova, and Gina M. Cannarozzi

in Codon Evolution: Mechanisms and Models

Published in print:
2012
Published Online:
May 2015
ISBN:
9780199601165
eISBN:
9780191810114
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:osobl/9780199601165.003.0013
Subject:
Biology, Evolutionary Biology / Genetics

This chapter introduces the biological causes of codon usage bias and summarizes various indices that have been developed to measure codon bias. It unifies the notation of these codon bias indices to ... More


Molecular Population Genetics

Daniel L. Hartl

in A Primer of Population Genetics and Genomics

Published in print:
2020
Published Online:
August 2020
ISBN:
9780198862291
eISBN:
9780191895074
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198862291.003.0007
Subject:
Biology, Biomathematics / Statistics and Data Analysis / Complexity Studies, Evolutionary Biology / Genetics

Chapter 7 is an introduction to molecular population genetics that includes the principal concepts of nucleotide polymorphism and divergence, the site frequency spectrum, and tests of selection and ... More


Detection and analysis of conservation at synonymous sites

Nimrod D. Rubinstein and Tal Pupko

in Codon Evolution: Mechanisms and Models

Published in print:
2012
Published Online:
May 2015
ISBN:
9780199601165
eISBN:
9780191810114
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:osobl/9780199601165.003.0014
Subject:
Biology, Evolutionary Biology / Genetics

This chapter describes several causes of codon usage bias, namely translational selection, mRNA structure, overlapping genes, and splicing signals. It provides an overview of the implications of ... More


The application of population genetics in the study of codon usage bias

Kai Zeng

in Codon Evolution: Mechanisms and Models

Published in print:
2012
Published Online:
May 2015
ISBN:
9780199601165
eISBN:
9780191810114
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:osobl/9780199601165.003.0016
Subject:
Biology, Evolutionary Biology / Genetics

This chapter examines codon usage bias, particularly synonymous polymorphisms, from a population genetic point of view. It describes the two most widely used models in the study of synonymous ... More


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