[Biococoa-dev] BCSequence

[Koen van der Drift]

On Aug 23, 2004, at 12:10 PM, John Timmer wrote:

> And I'll see if I can't look up some values for the nucleotides.
> Koen, since this is your field:  for the average mass of the ambiguous
> nucleotides, I was just averaging all possible nucleotides (ie, for Y, 
> I
> took the average of the values for C and T).  Since monoisotopic mass 
> is
> supposed to not be an average, should I return 0 for those cases?
>

I have already found the values, and will edit the plist tonight. You 
cannot average mass values (at least not for mass spec data), I suggest 
we'll leave them empty for the time being, and think of a solution. One 
question, the DNA-nucleotides are actually deoxy-nucleotides (I hope I 
didn't say anything stupid here :), so they are an oxygen short. But 
there are no deoxy's listed in the plist, so when you use a adenine, 
which one are you referring to? This is important to input the correct 
massvalues.


thanks,

- Koen.