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Motif finding is one of the NP-complete problems in Computational Biology.Existing nondeterministic algorithms for motif finding do not guarantee theglobal optimality of results and are sensitive to initial parameters. Toaddress this problem, the PROJECTION algorithm provides a good initial estimatethat can be further refined using local optimization algorithms such as EM,MEME or Gibbs. For large enough input (600-1000 bp per sequence) or forchallenging motif finding problems, the PROJECTION algorithm may run in aninordinate amount of time. In this paper we present a parallel implementationof the PROJECTION algorithm in Graphics Processing Units (GPUs) using CUDA. Wealso list down several major issues we have encountered including performingspace optimizations because of the GPU's space limitations.

PROJECTION Algorithm for Motif Finding on GPUs