[Biococoa-dev] MW of DNA with ambiguous bases

Koen van der Drift kvddrift at earthlink.net
Tue Sep 7 21:36:02 EDT 2004


I'm working on some code in BCMassCalculator that takes care of 
ambigous bases. First I test to see if it is an ambiguous base as 

         if ( [aSymbol isKindOfClass: [BCNucleotideDNA class]] && ! 
[(BCNucleotideDNA *) aSymbol isSingleBase])

Is that correct?

If true, it calculates a min and max value, based on the masses of the 
bases returned by representingBases and adds that to totalMin and 
totalMax. The new calculateMassWithRange returns an NSArray of two 
NSNumbers based on totalMin and totalMax, that can be interpreted by 
the client as needed.

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 ;-)


- Koen.

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