[Biococoa-dev] MW of DNA with ambiguous bases

[Koen van der Drift]

On Sep 7, 2004, at 10:04 PM, John Timmer wrote:

>>
>> Now I need some DNA sequence that contains ambigous bases, so I can
>> test this. Could someone paste some sequence for me (not too long, I'm
>> still on dial-up ;-)
>
> GAATTCNRYYRNMKGAATTCHVDBGAATTC
>
> That shouldn't stress the dialup.
>

Great - I've got the code working.

Now to implement it seamlessly in the rest of the code, here's what I 
propose.

Instead of returning a float, the molecularWeight method will now 
return an NSArray (or NSDictionary) with a minimal mass and maximum 
mass. If there are no ambigous symbols, both values will be the same, 
if they are they will differ. This is a much better solution then using 
the value zero for unambigous bases, that will give a much too low MW.

The same code can be used for any BCSequence, which makes everything 
much simpler.  We can remove the molecularWeight from BCNucleotideDNA 
and from BCSequenceDNA as well as from the base template.plist.

Let me know what you think and I will add the changes to CVS.


cheers,

- Koen.