Detection and analysis of conservation at synonymous sites

Nimrod D. Rubinstein, Tal Pupko

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review


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 these factors specifically to the detection and analysis of conservation at synonymous sites. It discusses various codon-based evolutionary models that have recently been developed and their application to the detection of conserved synonymous sites.

Original languageEnglish
Title of host publicationCodon Evolution
Subtitle of host publicationMechanisms and Models
PublisherOxford University Press
ISBN (Electronic)9780191810114
ISBN (Print)9780199601165
StatePublished - 23 Feb 2012


  • Codon models
  • Codon usage bias
  • Conservation
  • Overlapping genes
  • Splicing signals
  • Synonymous sites
  • Translational selection
  • mRNA structure

All Science Journal Classification (ASJC) codes

  • Agricultural and Biological Sciences(all)


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