Author(s)

Malik Yousef^1,2, Jens Allmer^3,4, Waleed Khalifa^1,2

¹Computer Science, The College of Sakhnin, Sakhnin, Israel.
²The Institute of Applied Research, The Galilee Society, Shefa-’Amr, Israel.
³Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Turkey.
⁴Bionia Incorporated, IZTEKGEB A8, Urla, Turkey.

MicroRNAs (miRNAs) are short (~21 nt) nucleotide sequences that are either co-transcribed during the production of mRNA or are organized in intergenic regions transcribed by RNA polymerase II. In animals, Drosha, and in plants DCL1 recognize pre-miRNAs which set themselves apart by their characteristic stem loop (hairpin) structure. This structure appears important for their recognition during the process of maturation leading to functioning mature miRNAs. A large body of research is available for computational pre-miRNA detection in animals, but less within the plant kingdom. For the prediction of pre-miRNAs, usually machine learning approaches are employed. Therefore, it is necessary to convert the pre-miRNAs into a set of features that can be calculated and many such features have been described. We here select a subset of the previously described features and add sequence motifs as new features. The resulting model which we called MotifmiRNAPred was tested on known pre-miRNAs listed in miRBase and its accuracy was compared to existing approaches in the field. With an accuracy of 99.95% for the generalized plant model, it distinguishes itself from previously published results which reach an average accuracy between 74% and 98%. We believe that our approach is useful for prediction of pre-miRNAs in plants without per species adjustment.

MicroRNA Prediction, Plant, Bioinformatics, Machine Learning, Sequence Motifs

Yousef, M. , Allmer, J. and Khalifa, W. (2016) Accurate Plant MicroRNA Prediction Can Be Achieved Using Sequence Motif Features. Journal of Intelligent Learning Systems and Applications, 8, 9-22. doi: 10.4236/jilsa.2016.81002.