[Bioperl-l] IUPAC support for DNA alignment

Hilmar Lapp hlapp at gmx.net
Fri Jun 27 08:47:12 EDT 2008

Hi Alexie,

On Jun 27, 2008, at 6:02 AM, Alexie Papanicolaou wrote:

> Hello
> I'm the user who asked for it. I don't know of any conventions but  
> perhaps people can help on this?
> I'm not an expert at all but here is my opinion:
> If you don't know the codon position (or even if it is coding) then  
> you can't estimate the codon degeneracy. If you don't know the  
> frequency of the bases representated in the degenerate site then you  
> can't model it either on the DNA level. So any solution will be ad- 
> hoc.
> Regarding 2 base degenerate positions: My suggestion is that in a  
> situation of alignment between, say a polymorphic and non  
> polymorphic population for that site, and the user is interested in  
> the distance between the populations, it would make sense to have  
> the score to the full match.
> Regarding 3 bases: I don't really know (see N below) but I 'd go for  
> a full match again, assuming the user build the consensus.

are you suggesting that a determined and a degenerate site aligned  
pairwise should score as much as two determined sites?

My (possibly naive) default would be to average over all  
possibilities, each weighted by base frequency (if base frequencies  
are assumed unequal or independent), thus integrating out the  
uncertainty. (For standard matrices, I think this would also result in  
N receiving zero score.)

In the end though, maybe there should be an option for a user to just  
provide a substitution matrix?


: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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