[Biococoa-dev] MW of DNA with ambiguous bases

[Alexander Griekspoor]

I usually start hitting the acgt like an idiot to build my own dummy 
sequence. I guess most easy way to start is to generate a simple 
ACGTACGT and then add one or more ambiguous symbols to see if 
calculations are correct....
The list of symbols the method should support would be:
ACGTNWMYRKHVDB-?

Alex


Op 8-sep-04 om 3:36 heeft Koen van der Drift het volgende geschreven:

> Hi,
>
> 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 
> follows:
>
>         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 ;-)
>
>
>
> thanks,
>
>
> - Koen.
>
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>
>
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                     ** Alexander Griekspoor **
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              The Netherlands Cancer Institute
              Department of Tumorbiology (H4)
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                    E-mail: a.griekspoor at nki.nl
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       Microsoft is not the answer,
       Microsoft is the question,
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