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bioRxiv2025

Frequency Chaos Game Representation - Singular Value Decomposition for Alignment-Free Phylogenetic Analysis

This paper introduces "SVD-FCGR," a scalable and efficient frame-work for phylogenetic analysis using Singular Value Decomposition (SVD) on Frequency Chaos Game Representation (FCGR). Unlike traditional MSA techniques, SVD-FCGR handles large datasets with lower computational complexity. It supports both genome-wide and gene-specific analyses, as demonstrated with datasets of Japanese Encephalitis Virus (JEV), Hepatitis B Virus (HBV), Human Immunodeficiency Virus(HIV-1), and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). For COVID-19, gene-level analysis of surface glycoprotein highlighted mutations affecting viral adaptability, while the envelope gene remained conserved. The method produced detailed phylogenetic trees, surpassing tools like MEGA in resolution and scalability. Validation from the AF Project ranked it 11th among alignment-free methods, confirming its reliability and adaptability.

bioinformatics↗

bioRxiv2021

Contribution of quasi-fibrillar superstructures in peroxide quenching by collagen peptides derived from fish processing by-products and their application as natural food additives

This study attempts to identify the significant role played by the secondary structure of collagen-derived peptides that are involved in lipid peroxide quenching in food products. Collagen was extracted from the skin of Perch and swim bladder of Rohu at 45-78% efficiency. It was identified as type-I based on a high molecular weight (110kDa) and its ion-exchange elution profile. The collagen samples were enzymatically hydrolyzed and collagen hydrolysate (CH) was extracted with an efficiency of 0.67-0.74g/g of collagen. The CH samples displayed a molecular weight in the range of 8.2-9.7kDa and exhibited a higher abundance of charges resulting in higher solubility. The structural studies revealed that the CH peptides existed in polyproline-II helix and formed a mimic-triple helix in a wide range of pH. In neutral and alkaline pH, the mimic helices joined to form a hierarchical quasi-fibrillar network that was smaller than collagen fibrils but also more dynamic. The CH exhibited >95% degradation in 15h through simulated digestion. The CH were able to decrease peroxide formation by 84.5-98.9% in commercially available cod liver and almond oil and increased the shelf life of soya bean oil by a factor of 5 after 6 months of storage. The addition of CH to cultured cells quenched peroxide ions generated in situ and decreased stressor activity by a factor of 12. The reason behind the high efficacy of CH was deciphered to be the proximal charge stabilization by the quasi-fibrillar network, which allowed efficient peroxide quenching and long-term stability.

biochemistry↗