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. 2023:2673:341-356.
doi: 10.1007/978-1-0716-3239-0_24.

A Lean Reverse Vaccinology Pipeline with Publicly Available Bioinformatic Tools

Bart Cuypers  1   2 , Rino Rappuoli  3 , Alessandro Brozzi  4
Affiliations

A Lean Reverse Vaccinology Pipeline with Publicly Available Bioinformatic Tools

Bart Cuypers et al. Methods Mol Biol. 2023.

Abstract

Reverse vaccinology (RV) marked an outstanding improvement in vaccinology employing bioinformatics tools to extract effective features from protein sequences to drive the selection of potential vaccine candidates (Rappuoli, Curr Opin Microbiol 3(5):445-450, 2000). Pioneered by Rino Rappuoli and first used against serogroup B meningococcus, since then, it has been used on several other bacterial vaccines, varying during time the adopted bioinformatics tools. Based on our experience in the field of RV and following an extensive literature review, we consolidate a lean RV pipeline of publicly available bioinformatic tools whose usage is described in this contribution. The protein features, whose extraction is reported in this contribution, can be also the input in a matrix format for machine learning-based approaches.

Keywords: Antigen abundance; B cell epitopes; Bacteria; Core proteome; Reverse vaccinology; Subcellular location; T cell epitopes.

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References

    1. Rappuoli R (2000) Reverse vaccinology. Curr Opin Microbiol 3(5):445–450. https://doi.org/10.1016/S1369-5274(00)00119-3
    1. Dalsass M, Brozzi A, Medini D, Rappuoli R (2019) Comparison of open-source reverse vaccinology programs for bacterial vaccine antigen discovery. Front Immunol 10. https://doi.org/10.3389/fimmu.2019.00113
    1. Vernikos GS (2020) A review of pangenome tools and recent studies. In: Tettelin H, Medini D (eds) The pangenome: diversity, dynamics and evolution of genomes. Springer, Cham, pp 89–112. https://doi.org/10.1007/978-3-030-38281-0_4 - DOI
    1. Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, Brinkman FSL (2010) PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics (Oxford, England) 26(13):1608–1615. https://doi.org/10.1093/bioinformatics/btq249 - DOI - PubMed
    1. Teufel F, Almagro Armenteros JJ, Johansen AR, Gíslason MH, Pihl SI, Tsirigos KD, Winther O, Brunak S, von Heijne G, Nielsen H (2022) SignalP 6.0 predicts all five types of signal peptides using protein language models. Nat Biotechnol 40(7):1023–1025. https://doi.org/10.1038/s41587-021-01156-3 - DOI - PubMed - PMC

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