An Overview of Bioinformatics Tools and Resources in Allergy

Abstract

The rapidly increasing number of characterized allergens has created huge demands for advanced information storage, retrieval, and analysis. Bioinformatics and machine learning approaches provide useful tools for the study of allergens and epitopes prediction, which greatly complement traditional laboratory techniques. The specific applications mainly include identification of B- and T-cell epitopes, and assessment of allergenicity and cross-reactivity. In order to facilitate the work of clinical and basic researchers who are not familiar with bioinformatics, we review in this chapter the most important databases, bioinformatic tools, and methods with relevance to the study of allergens.

Food Allergen Epitope Mapping

“…With the help of the machine learning technique and currently available epitope databases, various bioinformatic methods have been developed to predict allergen epitopes in silico . Such prediction tools are easy, fast, and inexpensive to perform and can complement traditional techniques in epitope mapping and assessment of immunoreactivity and cross-reactivity of allergens …”

“…Moreover, T-cell epitope prediction that is solely based on MHC binding is less accurate because peptide binding to MHC is necessary but insufficient for T-cell recognition. A combination of prediction methods based on proteasomal processing, transporter associated with antigen processing, and MHC binding has resulted in a better predictive performance for CD8 + T-cell epitopes than any single prediction tool . However, prediction tools based on the MHC II processing pathway are not currently available for CD4 + T-cell epitopes.…”

Detection of Lectin Protein Allergen of Kidney Beans (Phaseolus vulgaris L.) and Desensitization Food Processing Technology

“…In recent years, with the rapidly increased number of recognized allergens and the development of bioinformatics, allergomics is exploring by analyzing the repertoire of allergens, including genetics, proteomics, metabolomics, etc., and would provide more sensitive information for the allergen and epitope prediction with the relatively higher throughput and faster omics characteristics . Except for the sequence analysis, the identification of B cell and T cell epitopes, and the evaluation of allergies and cross-reactivity, bioinformatics tools could also calculate or simulate lectin–protein, lectin–polysaccharide, and lectin–biomolecule interactions, which would provide a theoretical supplement for the explanation of the sensitization alterations. , …”

“…152 Except for the sequence analysis, the identification of B cell and T cell epitopes, and the evaluation of allergies and crossreactivity, bioinformatics tools could also calculate or simulate lectin−protein, lectin−polysaccharide, and lectin−biomolecule interactions, which would provide a theoretical supplement for the explanation of the sensitization alterations. 153,154 Mass spectrometry would be the most used method in allergomics, and the concept of targeted quantitative proteomics and absolute quantitative strategy has been actively developed and applied in the trace lectin detections in raw or processed foods. 155−157 Prior to sample injection into mass spectrometry, one-dimensional gel electrophoresis and twodimensional gel electrophoresis are more commonly used to reduce the complexity of proteins in biological samples, and now, the capillary electrophoresis and chromatographic methods have become more popular for sample preparation.…”

Integrated approaches in diagnostics and therapy of allergic diseases

“…Ресурсы биоинформатики в аллергологии посвящены различным задачам: созданию и не-прерывному обновлению аллергенов в базах дан-ных, основным характеристикам аллергенов: молекулярный вес [7], структурные особенности, сезонность, наличие в пищевых продуктах [8], географическая распространенность [9]. Исполь-зование данных ресурсов позволяет клиницистам в диагностике и выборе специфической терапии, а исследователям -в целенаправленном выборе дизайна эксперимента.…”