Title: Derivative scores from site accessibility and ranking of miRNA target predictions

Authors: Abu Z.M. Dayem Ullah; Sudhakar Sahoo; Kathleen Steinhöfel; Andreas A. Albrecht

Addresses: Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK ' Molecular Diagnostics Laboratory, Aarhus University Hospital, Aarhus 8200, Denmark ' Department of Informatics, King's College London, London WC2R 2LS, UK ' Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7BL, UK

Abstract: In the present study, we define derivative scoring functions from PITA and STarMir predictions. The scoring functions are evaluated for up to five selected miRNAs with a relatively large number of validated targets reported by TarBase and miRecords. The average ranking of validated targets returned by PITA and STarMir is compared to the average ranking produced by the new derivatives scores. We obtain an average improvement of 13.6% (STD∼5.7%) relative to the average ranking of validated targets produced by PITA and STarMir.

Keywords: microRNA; RNA secondary structure; target prediction; multi-objective optimisation; Pareto front; site accessibility; ranking predictions; bioinformatics; binding regions; duplex conformations.

DOI: 10.1504/IJBRA.2012.048966

International Journal of Bioinformatics Research and Applications, 2012 Vol.8 No.3/4, pp.171 - 191

Published online: 05 Dec 2014 *

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