miRNA target prediction

  1. miRanda

The mirSVR score provided at mircrorna.org is the best tool for making predictions, as it utilizes the most recent miRanda prediction rules such as seed-site pairing, site context, free-energy, and conservation. I would recommend a mirSVR cutoff of <= -1.2. This value represents the top 5% of miRSVR scores, where the expected probability of observing a log expression change of <=.5 is ~50%, or of <=0.1 is 70%. The authors of the SVR score also suggest conservation as merely another factor to consider when determining the overall confidence of the prediction, and not as an absolute cut off.

Also if you are using miRanda locally on your own sequences, the generally recommended values for pairing score is >150 and energy score < -7. However, others have used the more stringent values of a pairing score of >155 and an energy score of < -20. I’m hoping soon they will release an updated miranda algorithm that provides local calculation of mirSVR scores.

This reference describes how the mirSVR score was put together: Betel, D., Koppal, A., Agius, P., Sander, C. Leslie, C, et al. (2010) Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol, 11, R90.

[http://www.biostars.org/p/5998/]

 

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CHENTONG

CHENTONG
积微,月不胜日,时不胜月,岁不胜时。凡人好敖慢小事,大事至,然后兴之务之。如是,则常不胜夫敦比于小事者矣!何也?小事之至也数,其悬日也博,其为积也大。大事之至也希,其悬日也浅,其为积也小。故善日者王,善时者霸,补漏者危,大荒者亡!故,王者敬日,霸者敬时,仅存之国危而后戚之。亡国至亡而后知亡,至死而后知死,亡国之祸败,不可胜悔也。霸者之善著也,可以时托也。王者之功名,不可胜日志也。财物货宝以大为重,政教功名者反是,能积微者速成。诗曰:德如毛,民鲜能克举之。此之谓也。

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