[Biojava-dev] Comments about OrderNDistributions

[Schreiber, Mark]

Hi,

To do a joint probability you just need to create a standard
Distribution over the (DNA x DNA x DNA) alphabet (if you want codons).
The OrderNDistribution was created specifically to handle conditional
probability (and probably should have a different name).

- Mark


> -----Original Message-----
> From: Francois Pepin [mailto:fpepin at cs.mcgill.ca] 
> Sent: Tuesday, 4 March 2003 2:06 p.m.
> To: biojava-dev at biojava.org
> Subject: [Biojava-dev] Comments about OrderNDistributions
> 
> 
> After going through the code for the OrderNDistributions, 
> there are a couple of comments and questions that I would have:
> 
> Is there any reason why the conditional probabilities instead 
> of joint probabilities are used there?
> 
> Right now, for OrderNDistribution.getWeight(cgt) (or any codon) gives
> P(t|cg) while getting P(cgt) would be a lot more useful. It's 
> quite easy to go from the joint to the conditional 
> probabilities while getting the opposite information is 
> pretty troublesome.
> 
> To get P(cgt), one would need to get P(t|cg)*sum of 
> P(g|nc)*sum of P(c|nn). (sum of 
> P(g|nc)=P(g|ac)+P(g|cc)+P(g|gc)+P(g|tc) ).
> 
> I don't really see why not store it as joint probabilities 
> and not have to worry about the conditioning and conditioned 
> alphabets there.
> 
> Also, I'm not positive about this, but it seems that some 
> information would be lost (or at least quite difficult to 
> recover) about the first few characters of the distribution, 
> for example with AACCCGGG, it there are no A's that would 
> appear anywhere in a 3rd order (which would really be a 2nd 
> order Markov chain) distributions. Two ways of going around 
> it would be to carry all of the distributions of lower order 
> to make sure that you have the data around, but it's a bit 
> cumbersome, or to have the 
> SymbolListViews.orderNSymbolList(AACCCGGG, 3) give out 
> NNAACCCGGG in this case, and have the orderNDistributions 
> keep that into account.
> 
> What do people think about this?
> 
> Francois Pepin
> 
> 
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