Efficient computation of optimal oligo-RNA binding.

@article{Hodas2004EfficientCO,
  title={Efficient computation of optimal oligo-RNA binding.},
  author={Nathan O. Hodas and Daniel P. Aalberts},
  journal={Nucleic acids research},
  year={2004},
  volume={32 22},
  pages={
          6636-42
        }
}
We present an algorithm that calculates the optimal binding conformation and free energy of two RNA molecules, one or both oligomeric. This algorithm has applications to modeling DNA microarrays, RNA splice-site recognitions and other antisense problems. Although other recent algorithms perform the same calculation in time proportional to the sum of the lengths cubed, O((N1 + N2)3), our oligomer binding algorithm, called bindigo, scales as the product of the sequence lengths, O(N1*N2). The… CONTINUE READING

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Introduction to Computational Molecular Biology, Chap

J. Meudanis, J. C. Setubal
  • 1997
VIEW 3 EXCERPTS
HIGHLY INFLUENTIAL

Genomes, 2nd ed

T. A. Brown
  • 2002
VIEW 1 EXCERPT