[Biococoa-dev] BCSequence

John Timmer jtimmer at bellatlantic.net
Mon Aug 23 18:01:57 EDT 2004

>> 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.

No, you have that exactly right - this is all DNA, so assume deoxyribose.
We can deal with RNA some other time.

Now, my chance to say something potentially stupid -
So both values you are using are specific for Mass Spec?  If so, I'd guess
we want a third, which is just the basic molecular weight, suitable for
calculating kD or size on a protein gel.  That's what I already have in
place for the bases, so I guess you can leave that there and add your keys
under the names you've been using.  I'll dig up the average molecular
weights for amino acids and add them sometime after you commit your version
with the names.  



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