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Splice Junction Identification using Long Short-Term Memory Neural Networks

Author(s):

Kevin Regan, Abolfazl Saghafi * and Zhijun Li  

Abstract:


Background: Splice junctions are the key to going from pre-messenger RNA to mature messenger RNA in many multi-exon genes due to alternative splicing. Since the percentage of multi-exon genes that undergo alternative splicing is very high, identifying splice junctions is an attractive research topic with important implications.

Objective: The aim is to develop a deep learning model capable of identifying splice junctions in RNA sequences using 13,666 unique sequences of primate RNA.

Method: A Long Short-Term Memory (LSTM) Neural Network model is developed that classifies a given sequence as EI (Exon-Intron splice), IE (Intron-Exon splice), or N (No splice). The model is trained with groups of trinucleotides and its performance is tested using validation and test data to prevent bias.

Results: Model performance was measured using accuracy and f-score in test data. The finalized model achieved an average accuracy of 91.34% with an average f-score of 91.36% over 50 runs.

Conclusion: Comparisons show a highly competitive model to recent Convolutional Neural Network structures. The proposed LSTM model achieves the highest accuracy and f-score among published alternative LSTM structures.

Keywords:

Splice Junction, Deep Learning, Neural Networks, LSTM, RNA-seq, Classification

Affiliation:

Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, Department of Mathematics, Physics and Statistics, University of the Sciences, Philadelphia, PA, Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA



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