[Biococoa-dev] Base test

[Alexander Griekspoor]

Koen,

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 
specificity.
I hope this helps, but perhaps I completely misunderstood the question.
Alex

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.
>
> _______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biococoa-dev
>
>
*********************************************************
                     ** Alexander Griekspoor **
*********************************************************
               The Netherlands Cancer Institute
               Department of Tumorbiology (H4)
          Plesmanlaan 121, 1066 CX, Amsterdam
                    Tel:  + 31 20 - 512 2023
                   Fax:  + 31 20 - 512 2029
                   AIM: mekentosj at mac.com
                  E-mail: a.griekspoor at nki.nl
               Web: http://www.mekentosj.com

               4Peaks - For Peaks, Four Peaks.
        2004 Winner of the Apple Design Awards
                Best Mac OS X Student Product
              http://www.mekentosj.com/4peaks

*********************************************************