High‐Throughput Analysis

Abstract

Modern biology is experiencing a rapid increase of data volumes that challenges our analytical skills and existing cyberinfrastructure. Exponential expansion of the Protein Sequence Universe (PSU), a protein sequence space, together with complexities of manual creation creates a major bottleneck in a biomedical research which requires a fusion of novel analytical approaches and computational means. Comprehensive visualization tool can be instrumental in meeting the need for functional annotation. Current existing resources lack scalable visualization tools to study the structure of the PSU. Here, we describe a multi-dimensional scaling (MDS) implementation to create a 3D embedding of the PSU. Applying the method to the prokaryotic PSU shows that MDS is capable of preserving important grouping structure such as relative proximity of functionally similar clusters, and a clear structural separation between clusters with specific and general functions. We also discuss the merits of the method including its scalable implementation and its role as a protein annotation tool that could help alleviate major bottleneck issue in modern biology. In conclusions, we emphasize the need for a transdisciplinary approach to quickly and efficiently translate the influx of new data into tangible innovations and long-awaited treatments.