[Biopython] CAI confusion

[Björn Johansson]

Hi,

I am trying to use the Bio.SeqUtils.CodonUsage module to calculate CAI for
S. cerevisiae genes.
Biopython comes with the SharpEcoliIndex from
Bio.SeqUtils.CodonUsageIndices, but none for S. cerevisiae.

I found one here:
http://downloads.yeastgenome.org/unpublished_data/codon/s_cerevisiae-codonusage.txt
and here:
http://downloads.yeastgenome.org/unpublished_data/codon/ysc.orf.cod

I parsed the first table which have the following format, unfortunately w/o
headers:

Gly	GGG	17673	6.05	0.12
Gly	GGA	32723	11.20	0.23
Gly	GGT	66198	22.66	0.46
Gly	GGC	28522	9.76	0.20
	
Glu	GAG	57046	19.52	0.30
...

ĩ believe the last column is the fraction. I think biopython expects
instead relative adaptedness w as indata for each codon.

 <https://paperpile.com/shared/V6j5yN>see
http://www.ncbi.nlm.nih.gov/pubmed/3547335

How do I calculate w from the frequency? Are there any examples or
code avaliable? I googled, but could not find anything.

grateful for help!

/bjorn










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Björn Johansson
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