A Convolutional Deep Learning Approach to identify DNA Sequences for Gene Prediction
Motta, J. A.; Gomez, P. D.
Show abstract
In this work, we present a highly efficient machine learning method for identifying DNA sequences that code for genes. The learning process is based on Human Genome Build 38 (GRCh38) sequences extracted from various specialized databases. The sequences were then translated into amino acid sequences and used to build matrices that facilitate the extraction of features with the TF*IDF metric for the creation of the training space. The prediction functions are learned using a convolutional neural network (CNN) deep learning model. The training spaces were created using the 24 chromosomes of the human genome and approximately 36,000 genes and pseudogenes whose names were fetched from the HUGO Gene Nomenclature Committee (HGNC). Performance analysis was performed on 24 genes associated with genetic disorders, as well as the surrounding DNA regions. The metrics used were precision, recall, F_score measure, accuracy and ROC curves for the genes of interest. The results achieved exceed all our expectations and place the work at the level of the state of the art for gene prediction.
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