Authors:
Hasan Oğul
1
;
Sinan U. Umu
2
;
Y. Yener Tuncel
3
and
Mahinur S. Akkaya
4
Affiliations:
1
Başkent University, Turkey
;
2
Middle East Technical University, Informatics Institute and Middle East Technical University, Turkey
;
3
Informatics Institute and Middle East Technical University, Turkey
;
4
Middle East Technical University, Turkey
Keyword(s):
MicroRNA target prediction, Markov chains.
Related
Ontology
Subjects/Areas/Topics:
Artificial Intelligence
;
Biomedical Engineering
;
Biomedical Signal Processing
;
Computational Intelligence
;
Health Engineering and Technology Applications
;
Human-Computer Interaction
;
Methodologies and Methods
;
Neural Networks
;
Neurocomputing
;
Neuroinformatics and Bioinformatics
;
Neurotechnology, Electronics and Informatics
;
Pattern Recognition
;
Physiological Computing Systems
;
Sensor Networks
;
Signal Processing
;
Soft Computing
;
Theory and Methods
Abstract:
Elucidation of microRNA activity is a crucial step in understanding gene regulation. One key problem in this effort is how to model the pairwise interaction of microRNAs with their targets. As this interaction is strongly mediated by their sequences, it is desired to set up a probabilistic model to explain the binding between a microRNA sequence and the sequence of a putative target. To this end, we introduce a new model of microRNA-target binding, which transforms an aligned duplex to a new sequence and defines the likelihood of this sequence using a Variable Length Markov Chain. It offers a complementary representation of microRNA-mRNA pairs for microRNA target prediction tools or other probabilistic frameworks of integrative gene regulation analysis. The performance of present model is evaluated by its ability to predict microRNA-mRNA interaction given a mature microRNA sequence and a putative mRNA binding site. In regard to classification accuracy, it outperforms a recent method
based on support vector machines.
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