[Biococoa-dev] Factories

Alexander Griekspoor mek at mekentosj.com
Mon Aug 30 02:13:38 EDT 2004

Oops, classical mistake from us DNA people :-) Indeed, a stop amino 
acid doesn't exist, only a stop codon. The encoded tRNA doesn't have an 
amino acid attached, therefore the ribozyme falls off the mRNA and 
translation is terminated. So conceptually adding a stop amino acid is 
not right here.
I think we should implement the intermediate layer here, which was a 
good thing to do anyway: the BCCodon and BCAlphabet objects.
BCCodon's are objects containing three BCSymbols sized BCSequenceDNA 
(or perhaps RNA to be more precise actually), which can also act as 
their identifier, and a BCSymbol of type aminoacid. A group of BCCodons 
forms a species specific BCAlphabet which contains the species name, 
and serves as the central point to pass around in translation methods, 
and can be generated by an AlphabetManager. The AphabetManager allows 
manipulation of the BCAlphabet objects and also facilitates the 
creation of predefined commonly used alphabets (from a plist).

I'm just thinking a bit out loud here about the following. In 4Peaks I 
get a nucleotide sequence derived from the trace file, which I 
"translate" to a protein sequence. But commonly this indeed contains a 
lot of stops: ACTW*GGH*LAK etc. By definition this is can not be a 
protein as Koen nicely mentioned. Perhaps we can make BCCodon a 
subclass of BCSymbol as well (I think that makes sense) and add a 
BCSequence subclass called BCSequenceCodons. I think this can greatly 
help in implementing translations and also in things like ORF finding.  
The nice thing here is that we can model the Protein Sequence as a real 
protein in which we don't have to think about what to do with stops in 
calculations like pI.

The flowchart would be as follows then:

BCSequenceDNA -> BCSequenceRNA -> BCSequenceCodons -> BCSequenceProtein

- every '->' is a translation step.
- of course we can make a number of convenience methods that would 
allow to do BCSequenceDNA -> BCSequenceProtein or BCSequenceRNA -> 
BCSequenceProtein with parameters to define what to do when a stop is 

I would love to see what you guys think....

>> I'll try it out tomorrow, but the last version I got doesn't have a 
>> stop
>> codon, which would be useful (especially as I'm designing 
>> translations right
>> now ;).
> Feel free to add that, I'm not that familiair with stop codons. Could 
> you explain to me why they should be in BCAminoAcid? I thought they 
> are part of a nucleotide sequence, not a protein.
> - Koen.
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                       ** Alexander Griekspoor **
                 The Netherlands Cancer Institute
                 Department of Tumorbiology (H4)
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                    AIM: mekentosj at mac.com
                     E-mail: a.griekspoor at nki.nl
                 Web: http://www.mekentosj.com

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