[Biococoa-dev] Weighted sequence score

Philipp Seibel biococoa at bioworxx.com
Tue Mar 15 18:03:55 EST 2005

Am 15.03.2005 um 23:36 schrieb 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.

i understand, i just wanted to differentiate to what is called 
"sequence weighting" which
is a method to give weights to complete sequences.

> 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.

Yes you are right, i was just thinking of the original meaning of a 
sequence profile. Of course a profile
can represent several thousand sequences, so the user shouldn't need to 
create the profile with all these
sequences. There has to be a method to set the percentage for one 
specific position of course.

just wanted to be sure that we are talking about, what usually is 
called sequence profile. ;-)


>> 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
> _______________________________________________
> This mind intentionally left blank

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