An accelerated Vidjil algorithm: up to 30X faster identification of V(D)J recombinations via spaced seeds and Aho-Corasick pattern matching

Abstract

VDJ recombination is a crucial process in the immune system, where a V (variable) gene, a D (diversity) gene, and a J (joining) gene are randomly combined to create unique antigen receptor genes. This process generates a vast diversity of antibodies and T-cell receptors, essential for recognizing and combating a wide array of pathogens. By identifying and quantifying these VDJ recombinations, we can gain a deeper and more precise understanding of the immune response, enhancing our ability to monitor and manage immune-related conditions