Efficient computation of optimal oligo-RNA binding.
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ABSTRACT:
SUBMITTER: Hodas NO
PROVIDER: S-EPMC545450 | biostudies-literature | 2004
REPOSITORIES: biostudies-literature
Publications
Efficient computation of optimal oligo-RNA binding.
Hodas Nathan O NO Aalberts Daniel P DP
Nucleic acids research 20041217 22
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 algor ...[more]
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