Efficient use of accessibility in microRNA target prediction.

ABSTRACT: Considering accessibility of the 3'UTR is believed to increase the precision of microRNA target predictions. We show that, contrary to common belief, ranking by the hybridization energy or by the sum of the opening and hybridization energies, used in currently available algorithms, is not an efficient way to rank predictions. Instead, we describe an algorithm which also considers only the accessible binding sites but which ranks predictions according to over-representation. When compared with experimentally validated and refuted targets in the fruit fly and human, our algorithm shows a remarkable improvement in precision while significantly reducing the computational cost in comparison with other free energy based methods. In the human genome, our algorithm has at least twice higher precis

SUBMITTER: Marin RM 

PROVIDER: S-EPMC3017612 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature