hauckl at mail.science.orst.edu
Wed Mar 13 20:27:00 EST 2002
My name is Laura Hauck and I am a pre-doctoral grad student at
Oregon State University. I have recently been using your Emboss
application to generate CAI values for several genes of interest that
emerged from a symbiotic relationship. I find that my values are a bit
odd. I have Codon Bias tables in Wisconsin Package format that I shifted
the columns around to look like the appropriate format of .cut files. The
program seems to accept that. The order of the codons, however, does not
match the codon order of the .cut tables that you supply (no, my model
organisms are not on the list...). Will this interfere with the analysis?
What is a good 'HI' value? I generated a codon bias table with one gene,
ran a CAI analysis with that table and that gene and got a value of 0.643.
That seemed low, is it? The codons should have matched exactly, I was
expecting a value of 1.0. Please let me know how to appropriately format
my tables if this sounds like an error result, or let me know what you
think may be wrong.
- Laura Hauck
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