[Biococoa-dev] BCSequence

[Koen van der Drift]

On Aug 23, 2004, at 6:01 PM, John Timmer wrote:

>

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

Thanks, I will add the values.


>
> 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.


There is no need for a third field, for calculating the kD of large 
biopolymers use the averageMass value. The Molecular Weight value has 
no additional information. For calculating peptide masses (eg after a 
protein digest) use the monoisotopic value. The same for 
oligonucleotides.


- Koen.