[Biococoa-dev] Base test

Alexander Griekspoor mek at mekentosj.com
Sat Aug 14 09:22:12 EDT 2004


The problem is not so much with complement bases but with the fact that 
the nucleotide alphabet contains ambiguous bases, bases that represent 
a group of bases. Examples are N for aNy base, but also R for puRine 
bases (A and G), W for Weak bases (A and T), etc. Therefore, each 
symbol has a -(NSArray *)matches; method that returns all bases that 
belong to this base (it returns only self if the base is atomic (A, C, 
G and T). A similar setup can be choosen for the complements of course, 
but perhaps it's indeed better to just return the complement ambiguous 
base. So N would return N as complement, W would return S as 
complement. I don't know if John plans to follow this latter setup 
actually, but he will probably tell us. In the protein world one could 
have a "stop" amino acid which would be ambiguous for the three stop 
codons we have, although another complicated factor would be species 
I hope this helps, but perhaps I completely misunderstood the question.

Op 14-aug-04 om 14:08 heeft Koen van der Drift het volgende geschreven:

> On Aug 13, 2004, at 10:57 AM, John Timmer wrote:
>>   During base initialization, I was going to create the
>> arrays of complements and representations.  This means every time the 
>> first
>> base was created, it would necessarily create its complement, all 
>> relevant
>> ambiguous bases, etc.
> I'm just a stupid chemist, could you explain to me why you need to 
> create arrays of complements, representations and ambiguous bases for 
> each base and what they are?
> (I do know that each base has a complement and what DNA looks like, 
> but don't understand why you'd need an array for each base, or did you 
> mean to create a complement sequence dynamically?)
> thanks,
> - Koen.
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                     ** Alexander Griekspoor **
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