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A probabilistic MCMC algorithm to find motifs in DNA

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COMP3456 - Assignment 1: Gibbs sampler for Motif Finding

Hi Mike.

It's me, Alex's Gibbs sampler.


You can run me like this:

mike@mikebox:$ (python|pypy) sampler.py file l k n

     file = <input file containing DNA matrix> 
     l = <length of motif to search for> 
     k = <number of identical results needed to acquire "convergence">
     n = <number of times to re-run the algorithm from a random starting point>

Don't forget those parameters. It feels all weird when someone runs me without them. Or worse, with extras. Ew.

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