[Biococoa-dev] BCCodon bug (?)

Alexander Griekspoor mek at mekentosj.com
Tue Sep 7 02:38:47 EDT 2004

>> Sorry about that - that's a stop codon.  It was decided that we 
>> wouldn't
>> create a "stop" amino acid (I still think it would be convenient to 
>> do so),
>> so I used a nil amino acid reference as stop within a BCCodon.  Part 
>> of what
>> I need to do is to put the headerdoc in place, so this doesn't 
>> surprise
>> anyone, and to create a BCSequenceCodon in order to provide an 
>> interface for
>> generating BCSequenceProteins safely (ie - ending the sequence when 
>> it hits
>> a stop codon).
>> And go ahead and change the method name.
> So it's ok if I change the * to a -?
> BTW, I have no problems with adding another entry in aminoacids.plist 
> for a 'stop amino acid', I just had not heard of it and was confused 
> by that terminology. If you think it's beneficial for the translation 
> code, let's just add it.

I'm not absolutely against a stop amino acid, but the choice was a 
rational one, they simply don't exist. Again, we're in code here so 
nobody will stop us from doing so, and indeed perhaps we should, 
although I like the idea of returning nil (in fact that happens in real 
life as well, the stop tRNA returns no amino acid to the ribosome, 
which crashes and falls of the mRNA ;-)

The thing is that a mRNA of codon list can contain stops, a protein 
not. So there's no problem of defining a stop codon, but that opens up 
the possibility to create proteins that contain stops, for which we 
than have to account for in calculation/transformation methods etc....

The idea we have now if simple:

BCSequenceDNA/RNA -> BCSequenceCodon -> BCSequenceProtein
All manipulations you perform on things with stops still there (like 
displaying the "translation" of my sequence file in 4Peaks for 
instance, which often contains many stops due to reading errors 
(CTG*AG*WC etc)) should be done with BCSequenceCodon. The only thing we 
still have to think about is that it would be nice to have to 
possibility to either treat BCSequenceCodon as a DNA sequence or as a 
protein sequence. (for example having length return 9 (aminoacids) in 
the above example or 27 (nucleotides)).
  I'm not sure if this is possible though, perhaps with convenience 
methods (the superclass method that we choose to be either DNA or 
Protein specific, and additional methods like numberOfNucleotides and 

So in conclusion, if we want to add a stop aminoacid, it's fine with 
me, but I propose in that case to severely limit its use (like you 
can't create proteins with them). I'll leave that up to you guys...

> - Koen.
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                     ** 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

                             iRNAi, do you?


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