[Biojava-l] Null Model
mark.schreiber at agresearch.co.nz
Tue May 6 22:17:37 EDT 2003
I'd second both of those proposals
From: Thomas Down [mailto:thomas at derkholm.net]
Sent: Tue 6/05/2003 9:01 p.m.
To: Ren, Zhen
Cc: biojava-l at biojava.org
Subject: Re: [Biojava-l] Null Model
Once upon a time, on a computer far far away, Ren, Zhen wrote:
> The second part of the question is how to do this shown above using
> BioJava API. Notice although there is a null model behind this,
> it is actually never used. How would I use the null model here?
Well, it's easy to write some code which uses log odds.
Distribution dist = ...
Symbol sym = ...
double logodds = Math.log(dist.getWeight(sym)) -
I guess it wouldn't be a bad thing to have a utility
method on DistributionTools to do this. I'll add it,
if nobody objects.
WeightMatrixAnnotator doesn't seem to support log odds.
I guess it's because it came from a DNA world, where using
odds scores often (although no always) makes very little
difference. It should probably be more flexible. A neat
way to do this, mirroring the way the dynamic programming
algorithms handle this issue, would be to use the ScoreType
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