[Biojava-dev] Problem regarding ScoreType

[Andreas Prlic]

Hi Ian,

with the BioJava 3.0 release some of the URLs changed and the latest
javadocs  now are for BioJava 3. The class you are referring to is now
part of the biojava-legacy project. Its javadoc can be found at

http://www.biojava.org/docs/api171/org/biojava/bio/dp/ScoreType.Odds.html

Andreas



On Fri, Dec 31, 2010 at 1:52 AM, Ian Agius <agius.ian at gmail.com> wrote:
> Hi all,
> I'm new to BioJava and was checking out what the ScoreType
> Probability,Null_MODEL and ODDS do exactly. I was trying to access the API
> but some of the pages were down for a reason. Do you know how I can access
> them? Also do you know whats the difference betweens the mentioned
> scoretypes?
>
> Im building some Profile HMMs of a set of protein sequences. I want to
> compare an unknown sequence to a number of profiles that I have created, and
> then choose the most probable profile to determine the family type. Ive
> tried using both ODDS and PROBABILITY but I am unsure which one to use when.
> Also I had some negative probabilities (-0.26) when using PROBABILITY and
> various results when using odds (from 300.12 to 25.6).
>
> One of the links that was down:
> http://www.biojava.org/docs/api/org/biojava/bio/dp/ScoreType.Odds.html
>
> Happy new year to all
>
> regards Ian
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