TPMGene

TPMGene is a computational tool designed for the analysis of T-cell receptor (TCR) and B-cell receptor (BCR) repertoire data. These repertoires are crucial components of the adaptive immune system, responsible for recognizing and responding to a vast array of antigens. Analyzing the diversity and dynamics of these receptor repertoires can provide insights into immune responses, disease states, and the development of immunotherapies.

The software is developed to handle high-throughput sequencing data generated from TCR and BCR genes. It typically involves steps such as read trimming, sequence alignment, V(D)J gene segment assignment, and the reconstruction of full-length V(D)J sequences. TPMGene aims to provide accurate and efficient processing of this complex biological data, enabling researchers to identify clonotypes, quantify their abundance, and assess repertoire diversity.

Key functionalities often found in such tools include the ability to distinguish between productive and non-productive rearrangements, identify somatic hypermutation in BCR sequences, and compare repertoires across different samples or time points. The output of TPMGene can be used for various downstream analyses, including identifying expanded clones associated with specific immune challenges, tracking immune reconstitution after transplantation, or characterizing the immune landscape in tumors. Its development contributes to the growing field of immunoinformatics, facilitating deeper understanding of adaptive immunity through computational approaches.