Codon adaptation index (CAI) is one of them. To examine the CAI value of a gene, a reference table of RSCU (relative synonymous codon usage) values for highly expressed genes is compiled. I am not sure how to define highly-expressed genes? How you guys deal with it when you calculate CAI values?
You can estimate codon bias by DNAsp software, and import your sequences in FASTA format and do the codon bias test. You can find more information for interpretation of the results in the softwares' manual.
Refer following papers.
http://www.biomedcentral.com/1471-2105/9/65#B3
http://link.springer.com/article/10.1007%2Fs10482-005-9016-z
http://mic.sgmjournals.org/content/151/7/2175.long
Haev a look on the software ACUA http://www.bioinsilico.com/acua
It brings a set of higly-expresse genes from diferent organisms that can be selected from a list to calculate CAI.
Be aware of some bugs, though: the calculation of GC3% with ACUA must be checked, as the software calculates GC3% based on GC3 count divided by the whole sequence and not by the number of 3rd positions.
Indeed, there are many (really many!) codon usage measures. Some of them require defining a "reference" - as you have rightly mentioned. Of course it is not clear how to define such a reference gene set. The reference set will differ over different organisms. In addition we know that expression will differ even in one specific organism - depending on environmental factors and tissue type, etc. This is why other measures of codon usage bias (that don't require such a priori infomration) have been proposed. For example, even using the notion of entropy can be a great measure, not any worse than the popular CAI and RSCU. But it is important to understand what excactly you would like to measure by studying codon bias. This will dictate your method choice. Further, it is important to realize the assumptions behind the different measures. For example, there are different flavours of CAI, and other codon bias measures that each attempted to "improve" on previous "contenders". We recently wrote a book chapter trying to summarize all the different codon measures and comment on their properties: Roth, Anisimova and Cannarozzi (2012) in the book "Codon evolution: mechanism and methods" (OUP). You can find teh paper on my website:
http://people.inf.ethz.ch/anmaria/publications.html
It's a long chapter, but we were trying to be exhaustive... that was hard work!!
:-))
If you want to measure codon usage within and across species in genomic scale, you can use CodonO (http://sysbio.cvm.msstate.edu/CodonO/). SCUO represents the overall synonymous codon usage order for the sequence.
I strongly recomend to use a software call CodonW, you can download it from: http://codonw.sourceforge.net/. There is also a PhD thesis associated to it.
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