This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: All data available at. Received: FebruAccepted: JPublished: October 17, 2018Ĭopyright: © 2018 Dhar et al. PLoS Comput Biol 14(10):ĬNRS and Ecole Normale Superieure, FRANCE
ANOTHER WORD FOR REPERTOIRE SOFTWARE
Furthermore, we provide a command-line tool in an open-source software package ( ) implementing these ideas and providing easy prediction using our pre-fit models.Ĭitation: Dhar A, Davidsen K, Matsen FA IV, Minin VN (2018) Predicting B cell receptor substitution profiles using public repertoire data. We fit this model on a large public dataset and validate the robustness of our approach on two external datasets. Using this framework, we show that substitution profiles from similar clonal families can be leveraged together with simulated substitution profiles and germline gene sequence information to improve prediction. In this paper, we present the method “Substitution Profiles Using Related Families” (SPURF), a penalized tensor regression framework that integrates information from a rich assemblage of datasets to predict the clonal-family-specific substitution profile for any single input sequence. Given the public release of many high-quality large B cell receptor datasets, one may ask whether it is possible to use such data in a prediction model for clonal-family-specific substitution profiles. However, most often only a single sequence is recovered from each clonal family in a sequencing experiment, making it impossible to construct a clonal-family-specific substitution profile. These clonal-family-specific frequency profiles, called “substitution profiles”, are useful for studying the course of affinity maturation as well as for antibody engineering purposes. in the same “clonal family”) are released from the germinal center their amino acid frequency profile reflects the allowed and disallowed substitutions at each position. At the end of affinity maturation, a number of cells sharing the same ancestor (i.e.
B cells develop high affinity receptors during the course of affinity maturation, a cyclic process of mutation and selection.
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