The RCDI server is a web-application that calculates the Relative Codon
Deoptimization Index (RCDI) and an expected value of the RCDI for a set
of query sequences by generating random sequences with similar G+C
content and amino acid composition to the input. This expected RCDI
therefore provides a direct threshold value for discerning whether the
differences in the RCDI value are statistically significant and arise
from the codon preferences or whether they are merely artifacts that
arise from internal biases in the G+C composition and/or amino acid
composition of the query sequences.
The CAIcal server is web server freely available that performs several computations in relation to codon usage and the codon adaptation of DNA or RNA sequences to host organisms.
The E-CAI server is a web-application and an executable program that calculates the expected value of the Codon Adaptation Index (CAI) for a set of query sequences by generating random sequences with similar G+C content and amino acid composition to the input. This expected CAI therefore provides a direct threshold value for discerning whether the differences in the CAI value are statistically significant and arise from the codon preferences or whether they are merely artifacts that arise from internal biases in the G+C composition and/or amino acid composition of the query sequences.
The Highly Expressed Genes Database (HEG-DB) is a new genomic database developed by Puigb˛ et al. from the Evolutionary Genomics Group at Rovira i Virgili University of Tarragona. The HEG-DB includes the prediction of which genes are highly expressed in prokaryotic complete genomes under strong translational selection. The current version of the database contains general features for almost 200 genomes under translational selection, including the correspondence analysis of the relative synonymous codon usage for all genes, and the analysis of their highly expressed genes. For each genome, the database contains functional and positional information about the predicted group of highly expressed genes. This information can also be accessed using a search engine. Among other statistical parameters, the database also provides the Codon Adaptation Index for all of the genes using the codon usage of the highly expressed genes as a reference set. The "Pathway Tools Omics Viewer" from the BioCyc database enables the metabolic capabilities of each genome to be explored, particularly those related to the group of highly expressed genes.
For more details see the article Puigb˛ et al., Nucleic Acids Res., October 11, 2007; doi:10.1093/nar/gkm831.
PAL2NAL converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. Synonymous (Ks) and non-synonymous (Ka) substitution rates can be calculated.
Sliding Window Analysis of Ka and Ks (SWAKK) is tool for detecting positive selection in proteins usinga sliding window substitution rate analysis. The program can display the results on a 3D protein structure.
CodonO is a method for measuring synonymous codon usage bias within and across genomes.
Find GC content and frequency of codon usage for any organism that has a sequence in GenBank.
CorGenmeasures long-range correlations in DNA sequences and can generate random sequences with the same (or user-specified) correlation and composition parameters.
GC-Profile is a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences.
Graphical representation of codon bias
GenDecoder is a prediction server for animal mitochondrial genetic codes. It provides information about codon-usage, amino acid composition, GC content and a final genetic code prediction for a mitochondrial genome sequence.
JCAT (Java Codon Adaptation Tool) is a tool that can adjust the codon usage of an input sequence to the selected organism. Useful for improving the expression of foreign genes in hosts with different codon usage.
DyNAVacS is a tool for designing DNA vaccines that includes steps for chosing a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses, and providing additional sequence signals for efficient translation. It also allows includes restriction enzyme mapping and design of primers spanning user specified sequences.
Codon usage tables
Nakamura, Y., Gojobori, T. and Ikemura, T. (2000). Codon usage tabulated from the international DNA sequence databases: status for the year 2000. Nucl. Acids Res. 28, 292.