Journal Article

Integrated entropy-based approach for analyzing exons and introns in DNA sequences

Li, Junyi, Wang, Rongjie, Tan, Renjie, Liu, Bo, Li, Huinian, Ping, Yuan, Zhang, Li, Wang, Zhen, Wang, Yadong, Xu, Qingzhe

2019

Overview

Background Numerous essential algorithms and methods, including entropy-based quantitative methods, have been developed to analyze complex DNA sequences since the last decade. Exons and introns are the most notable components of DNA and their identification and prediction are always the focus of state-of-the-art research. Results In this study, we designed an integrated entropy-based analysis approach, which involves modified topological entropy calculation, genomic signal processing (GSP) method and singular value decomposition (SVD), to investigate exons and introns in DNA sequences. We optimized and implemented the topological entropy and the generalized topological entropy to calculate the complexity of DNA sequences, highlighting the characteristics of repetition sequences. By comparing digitalizing entropy values of exons and introns, we observed that they are significantly different. After we converted DNA data to numerical topological entropy value, we applied SVD method to effectively investigate exon and intron regions on a single gene sequence. Additionally, several genes across five species are used for exon predictions. Conclusions Our approach not only helps to explore the complexity of DNA sequence and its functional elements, but also provides an entropy-based GSP method to analyze exon and intron regions. Our work is feasible across different species and extendable to analyze other components in both coding and noncoding region of DNA sequences.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Algorithms / Analysis / Base Sequence / Bioinformatics / Biomedical and Life Sciences / Chromosomes, Human - genetics / Complexity / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Decomposition / Deoxyribonucleic acid / Digitization / DNA / DNA - genetics / DNA sequences / Entropy / Entropy (Information theory) / Exon and intron prediction / Exons / Exons (Molecular genetics) / Exons - genetics / Feasibility studies / Gene sequencing / Generalized topological entropy / Genes / Genetic research / Genome, Human / Genomes / Genomic signal processing / Humans / Information entropy / Information storage / Information theory / Introns / Introns - genetics / Life Sciences / Mathematical analysis / Methods / Microarrays / Nucleotide sequence / Ontology / Promoter Regions, Genetic - genetics / ROC Curve / Sequence Analysis, DNA - methods / Signal processing / Signal Processing, Computer-Assisted / Singular value decomposition / Studies / Topology