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bioRxiv · 10.1101/2023.01.30.526195

A Novel Approach to T-Cell Receptor Beta Chain (TCRB) Repertoire Encoding Using Lossless String Compression

Konstantinovsky, T.·Yaari, G.
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Abstract

T-cell diversity is crucial for producing effective receptors that can recognize the pathogens encountered throughout life. A stochastic biological process known as VDJ recombination accounts for the high diversity of these receptors, making their analysis challenging. We present a new approach to sequence encoding and analysis, based on the Lempel-Ziv 76 algorithm (LZ-76). By creating a graph-like model, we identify specific sequence features and produce a new encoding approach to an individuals repertoire. We demonstrate that this repertoire representation allows for various applications, such as generation probability inference, informative feature vector derivation, sequence generation, and a new measure for diversity estimation.

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Konstantinovsky, T., Yaari, G.. 2023-02-01. A Novel Approach to T-Cell Receptor Beta Chain (TCRB) Repertoire Encoding Using Lossless String Compression. https://doi.org/10.1101/2023.01.30.526195

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