Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach

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Abstract

Motivation: Proteins recognizing short peptide fragments play a central role in cellular signaling. As a result of high-throughput technologies, peptide-binding protein specificities can be studied using large peptide libraries at dramatically lower cost and time. Interpretation of such large peptide datasets, however, is a complex task, especially when the data contain multiple receptor binding motifs, and/or the motifs are found at different locations within distinct peptides.Results: The algorithm presented in this article, based on Gibbs sampling, identifies multiple specificities in peptide data by performing two essential tasks simultaneously: alignment and clustering of peptide data. We apply the method to de-convolute binding motifs in a panel of peptide datasets with different degrees of complexity spanning from the simplest case of pre-aligned fixed-length peptides to cases of unaligned peptide datasets of variable length. Example applications described in this article include mixtures of binders to different MHC class I and class II alleles, distinct classes of ligands for SH3 domains and sub-specificities of the HLA-A*02:01 molecule. © The Author(s) 2012. Published by Oxford University Press.

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Andreatta, M., Lund, O., & Nielsen, M. (2013). Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach. Bioinformatics, 29(1), 8–14. https://doi.org/10.1093/bioinformatics/bts621

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