CodonExplorer: an interactive online database for the analysis of codon usage and sequence composition.
The analysis of DNA composition and codon usage reveals many factors that influence the evolution of genes and genomes. In this chapter, we show how to use CodonExplorer, a web tool and interactive database that contains millions of genes, to better understand the principles governing evolution at the single gene and whole-genome level. We present principles and practical procedures for using analyses of GC content and codon usage frequency to identify highly expressed or horizontally transferred genes and to study the relative contribution of different types of mutation to gene and genome composition. CodonExplorer's combination of a user-friendly web interface and a comprehensive genomic database makes these diverse analyses fast and straightforward to perform. CodonExplorer is thus a powerful tool that facilitates and automates a wide range of compositional analyses.
Zaneveld
Jesse
J
Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA.
Hamady
Micah
M
Sueoka
Noboru
N
Knight
Rob
R
D001482:Base Composition; D001483:Base Sequence; D003062:Codon / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry*; D030561:Databases, Nucleic Acid; D022761:Gene Transfer, Horizontal; D020407:Internet; D008969:Molecular Sequence Data; D012984:Software
D003062:Codon; D004247:DNA