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With recent advancements in computational biology, high throughput Next-Generation Sequencing (NGS) has become a de facto standard technology for gene expression studies, including DNAs, RNAs, and proteins; however, it generates several millions of sequences in a single run. Moreover, the raw sequencing datasets are increasing exponentially, doubling in size every 18 months, leading to a big data issue in computational biology. Moreover, inflammatory illnesses and boosting immune function have recently attracted a lot of attention, yet accurate recognition of Anti-Inflammatory Peptides (AIPs) through a biological process is time-consuming as therapeutic agents for inflammatory-related diseases. Similarly, precise classification of these AIPs is challenging for traditional technology and conventional machine learning algorithms. Parallel and distributed computing models and deep neural networks have become major computing platforms for big data analytics now required in computational biology. This study proposes an efficient high-throughput anti-inflammatory peptide predictor based on a parallel deep neural network model. The model performance is extensively evaluated regarding performance measurement parameters such as accuracy, efficiency, scalability, and speedup in sequential and distributed environments. The encoding sequence data were balanced using the SMOTETomek approach, resulting in a high-accuracy performance. The parallel deep neural network demonstrated high speed up and scalability compared to other traditional classification algorithms study’s outcome could promote a parallel-based model for predicting anti-Inflammatory Peptides.