AllerHunter: a SVM-pairwise system for assessment of allergenicity and allergic cross-reactivity in proteins.
AllerHunter: a SVM-pairwise system for assessment of allergenicity and allergic cross-reactivity in proteins.
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DOI：
10.1371/journal.pone.0005861
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发表时间：
2009-06-10
期刊：
影响因子：
3.7
通讯作者：
Tammi MT
中科院分区：
文献类型：
--
作者：
Muh HC;Tong JC;Tammi MT
过敏是工业化国家的一个主要健康问题。转基因粮食作物的数量正在迅速增长，因此需要在将其引入人类食物链之前进行过敏性评估。虽然现有的生物信息学方法对于高度保守的序列已经取得了良好的准确性，但从过敏原样非过敏原序列中区分过敏原和非过敏原仍然很困难。我们描述了 AllerHunter，这是一个基于网络的计算系统，用于评估蛋白质的潜在过敏性和过敏交叉反应性。它将迭代成对序列相似性编码方案与 SVM 结合起来作为判别引擎。成对矢量化框架允许系统对涉及交叉反应的过敏原的基本特征进行建模，但不限于不同的物理化学特性集。该系统使用 1,356 个已知过敏原和 13,449 个假定的非过敏原序列进行了严格的训练和测试。为了验证预测模型，进行了广泛的测试。该系统可有效区分过敏原和非过敏原与过敏原样非过敏原序列。测试结果显示，AllerHunter 的敏感性为 83.4%，特异性为 96.4%（准确度 = 95.3%，受试者工作特征曲线下面积 AROC = 0.928±0.004，Matthew 相关系数 MCC = 0.738），明显优于现有的使用 1443 个蛋白的独立数据集的多种方法。序列。 AllerHunter 的网址为 http://tiger.dbs.nus.edu.sg/AllerHunter
Allergy is a major health problem in industrialized countries. The number of transgenic food crops is growing rapidly creating the need for allergenicity assessment before they are introduced into human food chain. While existing bioinformatic methods have achieved good accuracies for highly conserved sequences, the discrimination of allergens and non-allergens from allergen-like non-allergen sequences remains difficult. We describe AllerHunter, a web-based computational system for the assessment of potential allergenicity and allergic cross-reactivity in proteins. It combines an iterative pairwise sequence similarity encoding scheme with SVM as the discriminating engine. The pairwise vectorization framework allows the system to model essential features in allergens that are involved in cross-reactivity, but not limited to distinct sets of physicochemical properties. The system was rigorously trained and tested using 1,356 known allergen and 13,449 putative non-allergen sequences. Extensive testing was performed for validation of the prediction models. The system is effective for distinguishing allergens and non-allergens from allergen-like non-allergen sequences. Testing results showed that AllerHunter, with a sensitivity of 83.4% and specificity of 96.4% (accuracy = 95.3%, area under the receiver operating characteristic curve AROC = 0.928±0.004 and Matthew's correlation coefficient MCC = 0.738), performs significantly better than a number of existing methods using an independent dataset of 1443 protein sequences. AllerHunter is available at http://tiger.dbs.nus.edu.sg/AllerHunter
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