Allows rapid testing of hypotheses about codon usage in sequenced genes and genomes. CodonExplorer can reveal patterns associated with gene expression changes, mutational biases and horizontal gene transfer (HGT). It allows convenient discovery of genes by genome, function or orthology and visualization of the composition of these genes. This tool employs Monte Carlo techniques for testing the statistical significance of differences in codon usage or nucleotide sequence composition.
Department of Computer Science, University of Colorado, Boulder, CO, USA; AmGen, Longmont, CO, USA; Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA; Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA; Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA
CodonExplorer funding source(s)
Supported by NIH/CU Molecular Biophysics and Signaling & Cell Regulation Training Programs (T32GM065103 and T32GM08759, in part); NSF EAPSI fellowship (OISE0812861, in part); National Institutes of Health (P01DK078669, in part); CU URAP and HHMI/UROP scholarships (in part).