Classifying promoters by interpreting the hidden information of DNA sequences for disease prediction in clinical laboratories using Gaussian decision boundary estimation
Affiliations: [a] Department of CSE, SASTRA Deemed University, Thanjavur, Tamil Nadu, India | [b] Department of Artificial Intelligence and Data Science, Deep Learning Lab, Ramco Institute of Technology, Rajapalayam, Tamil Nadu, India | [c] School of Computer Science and Engineering, VIT Chennai Campus, Tamil Nadu, India | [d] Department of Computer Technical Engineering, College of Technical Engineering, The Islamic University, Najaf, Iraq
Correspondence:
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Corresponding authors: Pradeepa S, Department of CSE, SASTRA Deemed University, Thanjavur, TamilNadu, India. E-mail: [email protected]. Vimal Shanmuganathan, Deep Learning Lab, Department of Artificial Intelligence and Data Science, Ramco Institute of Technology, Rajapalayam, tamilnadu, India. E-mail: [email protected].
Abstract: A promoter is a brief stretch of DNA (100–1,000 bp) where RNA polymerase starts to transcribe a gene. A DNA (Deoxyribonucleic Acid) base pair is a fundamental unit of DNA structure and represents the pairing of two complementary nucleotide bases within the DNA double helix. The four DNA nucleotide bases are adenine (A), thymine (T), cytosine (C), and guanine (G). DNA base pairs are the building blocks of the DNA molecule, and their complementary pairing is central to the storage and transmission of genetic information in all living organisms. Normally, a promoter is found at the 5′ end of the transcription initiation site or immediately upstream. Numerous human disorders, particularly diabetes, cancer, and Huntington’s disease, have been shown to have DNA promoter as their root cause. The scientific community has long been interested in learning crucial information about protein-coding genes. Finding the promoters is therefore the first step in finding genes in DNA sequences. The scientific world has always been attracted by the effort to glean crucial knowledge about protein-coding genes. Consequently, identifying promoters has emerged as an intriguing challenge that has caught the interest of numerous researchers in the field of bioinformatics. We proposed Gaussian Decision Boundary Estimation in machine learning models to detect transcription start sites (promoters) in the DNA sequences of a common bacteria, Escherichia coli. The best features are identified through a score-based function to select relevant nucleotides that are directly responsible for promoter recognition, in order maximise the models’ performance. The Gaussian Decision Boundary Estimation based support-vector-machine model is trained with these features and finds the best hyperplane that separates the data into different classes. Throughout this study, promoter regions could be identified with high accuracy 99.9% which is better compared to other state of art algorithms. The comparison of machine learning classification models is another major emphasis of this paper in order to identify the model that most accurately predicts DNA sequence promoters. It provides analysis for further biological research as well as precision medicine.
