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neural network programming

 
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hi,
does anybody have experience in neural network programming with java (especially JOONE), or has taken a look at it....

my question is, which algorithm is most suitable, if I have a sequences of undetermined length (between 6 and 120 characters, like a peptide sequence) trained with it and I want it to recognize similar sequences within large protein sequences....

I know there maybe other methods to solve that problem...but I think it's a good and very fast approach for that problem
 
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