The codon bias index (cbi) is a statistic created by Bennetzen and Hall to quantify the extent to which more frequently used codons are used in preference to less frequently used codons.  The extent of usage of preferred codons was shown to correlate with the level of expression of the encoded gene for different proteins of yeast, E. coli1, and many other organisms.   Recently it has been suggested to correlate with relative expression levels of different isozymes.

CodonBiasIndex will calculate the cbi or the %GC of a segment of DNA, and will read small text files.  Double-click to run it, then choose what you want to do from the menus.  The File and Edit Menus allow you to work with small text files.  The Molecular Biology Menu allows you to choose to calculate codon bias indices or the %GC for a DNA sequence.  The ReadSeq Pascal source code is used to read DNA sequence text files in the EMBL, NBRF, GenBank, GCG, DNA Strider, Fitch, Pearson or Zuker formats.  CodonBiasIndex was created using Think Pascal 4.0 and the Think Class Library.

More complete documentation is included with the CodonBiasIndex program.

Tom Ritch
ritch@seas.ucla.edu