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I am calculating a certain statistic(relative entropy) of a certain sequence alignment over DNA sequences. The statistic has a certain distribution in the entire genome of which I only have 1000 sequences of length 1000. I want to test the significance of a certain value of the statistic but I obviously do not know the distribution of the statistic so I can't use t-test and such and I also have a sample of size 1000 from the population. I guess I could use non-parametric methods like bootstrapping and such to approximate the p-value of a certain statistic value but the research papers that I have been reading seem to use methods from Large Deviation Statistics and Fast Fourier Transforms. I have not have time to learn these concepts on my own and just need a nudge in the right direction. Any ideas ?

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Bootstrap sounds good to me. –  user10525 Apr 18 '12 at 10:43
    
Any ideas on something faster and more precise ? –  Farhad Apr 18 '12 at 23:07
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