AllerHunter A SVM-Pairwise System for Assessment of Allergenicity and Allergic Cross-Reactivity in Proteins 英文参考文献.docVIP

AllerHunter:ASVM-PairwiseSystemforAssessmentof AllergenicityandAllergicCross-ReactivityinProteins HonChengMuh1,JooChuanTong2,3,MarttiT.Tammi1,3,4 * 1Department of Biological Sciences, National University of Singapore, Singapore, Singapore, 2Data Mining Department, Institute for Infocomm Research, Singapore, Singapore, 3Department of Biochemistry, National University of Singapore, Singapore, Singapore, 4Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet,Stockholm,Sweden Abstract 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 bioinformaticmethodshaveachievedgoodaccuraciesforhighlyconservedsequences,thediscriminationofallergensand 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 vectorizationframeworkallowsthesystemtomodelessentialfeaturesinallergensthatareinvolvedincross-reactivity,but notlimitedtodistinctsetsofphysicochemicalproperties.Thesystemwasrigorouslytrainedandtestedusing1,356known allergen and 13,449 putative non-allergen sequences. Extensive testing was performed for validation of the prediction models.Thesystemiseffectivefordistinguishingallergensandnon-allergensfromallergen-likenon-allergensequences. TestingresultsshowedthatAllerHunter,withasensitivityof83.4%andspecificityof96.4%(accuracy=95.3%,areaunder the receiver operating characteristic curve AROC=0.92860.004 and Matthew’s correlation coefficient MCC=0.738), performssignificantlybetterthananumberofexistingmethodsusinganindependentdatasetof1443proteinsequences. AllerHunterisavailableat.sg/AllerHunter Citat