Codon Usage Bias Database (CUB-DB)

The Codon Usage Bias Database is a showcase for my bias measures, modified Self-Consistent Codon Index (mSCCI) and a direct search approach for codon adaptiveness (weights) using a genetic algorithm (GA). The first modifies the Carbone et al. SCCI algorithm to direct it toward translational efficiency bias instead of the dominant bias (mSCCI, Raiford et al.). The second searches for a set of weights that explain the expected high-placement of the reference set genes in a sorted list of genes by bias adherence score (Direct Search, Raiford et al.). This is the bias measure that I recommend you use if you wish to measure adherence to translational efficiency bias.

In addition to mSCCI and the search based approach, the database contains various other bias measures (SCCI, CAI, FOP, MCU, Nc, Scaled Χ^2, and tAI) for all of the genomes sequenced and stored on the NCBI Microbial Genomes Website. This database is synchronized with the NCBI database on a regular basis (roughly weekly) so that any sequenced microbial organism should be found on this site within a short time of its being published.

The database currently has a size of approximately 66Gig and is comprised mostly of text files residing on a filesystem. Statistics calculated on a genome-wide basis are stored in a MySQL database, while other data, such as gene-centered statistics, are stored on the filesystem.

The measures stored here are those for which I am most familiar. The implementations of the algorithms are my own (written in PERL, and in the case of the GA, in C++), and as such, are based upon my interpretation of their published methods. As the website grows I will include such things as mechanisms for user feedback so that errors in the data or suggestions for improving the site can be communicated to me.

The site will evolve over time, and additional methods and/or data will be included. Additionally, more and more context sensitive help will be added to make the site more user friendly.

I hope you find the site useful for your research.
Your friendly neighborhood codon usage guy,
Doug Raiford

The content and opinions expressed on this Web page do not necessarily reflect the views of nor are they endorsed by the University of Montana.