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Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements

Item Type:Article
Title:Assessing the utility of thermodynamic features for microRNA target prediction under relaxed seed and no conservation requirements
Creators Name:Lekprasert, P. and Mayhew, M. and Ohler, U.
Abstract:Many computational microRNA target prediction tools are focused on several key features, including complementarity to 5'seed of miRNAs and evolutionary conservation. While these features allow for successful target identification, not all miRNA target sites are conserved and adhere to canonical seed complementarity. Several studies have propagated the use of energy features of mRNA:miRNA duplexes as an alternative feature. However, different independent evaluations reported conflicting results on the reliability of energy-based predictions. Here, we reassess the usefulness of energy features for mammalian target prediction, aiming to relax or eliminate the need for perfect seed matches and conservation requirement.
Keywords:Algorithms, Computational Biology, Down-Regulation, Eukaryotic Initiation Factor-2, Gene Expression Profiling, Genomics, MicroRNAs, Viral RNA, Thermodynamics
Source:PLoS ONE
ISSN:1932-6203
Publisher:Public Library of Science (U.S.A.)
Volume:6
Number:6
Page Range:e20622
Date:6 June 2011
Official Publication:https://doi.org/10.1371/journal.pone.0020622
PubMed:View item in PubMed

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