Re: [Biojava-l] log-odds ratio

[Matthew Pocock]

The dynamic programing code all use log odds (or log probabilities for 
forwards/backwards training) for exactly this reason. I guess weight 
matricies should do this too. If you're searching with a long weight 
matrix, then you should probably be using a profile HMM though.

Matthew

Ren, Zhen wrote:
Hi, there,

The WeightMatrixDemo example at "BioJava In Anger" page (http://bioconf.otago.ac.nz/biojava/weightMatrix.htm?PHPSESSID=0adccafdabe1f2c52b062649c404c50f generates a WeightMatrix from an aligment and uses that matrix to annotate a Sequence with a threshold of 0.1.  This program uses the odds ratio.  I wonder if BioJava has the capacity to use the log-odds ratio (an additive scoring system) to avoid overflow.  So, I guess very slight modification can do the same thing as this program does.  Thanks.

Zhen

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