[Biococoa-dev] Weighted sequence score

[John Timmer]

>>> One of the things the alignment work has gotten me thinking about
>>> implementing is a weighted sequence score.
> 
> Its more a weighted base score, isn't it ?

Well, it should work for anything, although the examples I'm thinking of
using it for are bases.  That's just my personal bias, though.

Regarding what's below, I think it's a great idea as one alternative for
creating a weighted consensus, but it's not a general case.  There's
statistics generated from several hundred mammalian splice sites, which have
awkward fractions like 43%, and we'd need a way of having those imported
without forcing the user to create enough sequences to generate a 43%
fraction.


> A Profile is nothing else than a bunch of sequences represented by a
> "probabilistic" model. So if you look at it, like
> 80% of my sequences have at a specific position an A and 15% of them
> have a G, it will bring you to a convenient method like:
> 
> + (BCSequenceProfile *)profileWithSequenceArray:(NSArray *)array;
> 
>> Hmm, not really, but I don't have a good alternative either, perhaps
>> some "consensus site object".
> 
> Don't think we will need it, because you can construct a profile like
> this:
> 
> sequenceA : AAAATATAGC
> sequenceB : AAATATATAT
> sequenceC:  AAATTATATT
> 
> with the previous described method
> 
> A: 100
> A: 100
> A: 100
> A: 33 T: 66
> A: 33 T: 66
> ....
> 
> Of course profiles could have a convenient method like this:
> 
> + (BCSequenceProfile *)profileWithAlignment:(BCSequenceAlignment
> *)alignment;
> 
> Phil


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