Tamas Hegedus hegedus at biomembrane.hu
Tue Dec 20 13:17:18 UTC 2005


I am not a CAI expert; I also could not find one around me; reading was 
not enough for me in this topic.
So I would like to take the opportunity to ask a CAI (not EMBOSS) 
related question.

What can you tell me about human (mammalian) CAI tables?
What do you think/know about the FOP values introduced by Lavner & Kotlar?

I would like to use some measure to predict the translation speed of 
certain regions in some proteins I am interested in.


Peter Rice wrote:
> Kevin Brown wrote:
>>I've searched the archives and the Net trying to find more information
>>the list of highly-expressed genes that CAI used to create the codon
>>tables for the various species.  Does anyone know where these tables
>>came from?
> Well, it is a long story ...
> The original CAI (Codon Adaptation Index) was calculated for S. cerevisiae and 
> used a set of 24 genes (ribosomal proteins, for example) that were known to be 
> highly expressed.
> Many years ago when I wrote a program to calculate the codon usage for S. 
> pombe (fission yeast) in a program called "codfish", I created a table for the 
> few S. pombe genes from the same set that had already been sequenced.
> On arriving at the Sanger Centre, where they were sequencing a lot of S. 
> cerevisiae, I needed the codon usage table for the original CAI - and found 
> that when I used the current gene sequences I got the wrong answer.
> After some tweaking I was able to reconstruct the original versions of the 
> cerevisiae sequences and could reproduce the "standard" CAI values. The 
> differences were minor - mainly missed short 5' exons.
> The tables Eyeast_cai.cod and Eschpo_cai.cut are the result of these two 
> tables. There are, for historic reasons, copies of these tables with no 
> headers and different names which are "obsolete" and will disappear in EMBOSS 
> 4.0.0.
> As for "codfish" ... it implemented an algorithm from Frank Wright to 
> calculate the effective number of codons. Frank is a vegan (does not eat 
> codfish), so in EMBOSS we renamed it "chips" :-)
> Hope that helps!
> Peter
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