NDLI: AllerHunter: A SVM-Pairwise System for Assessment of Allergenicity and Allergic Cross-Reactivity in Proteins

Content Provider	PubMed Central
Author	Muh, Hon Cheng Tong, Joo Chuan Tammi, Martti T.
Editor	Rapallo, Fabio
Copyright Year	2009
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 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
Related Links	http://dx.doi.org/10.1371/journal.pone.0005861
Starting Page	5861
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	6
Volume Number	4
Language	English
Publisher	Public Library of Science
Publisher Date	2009-06-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

AllerHunter: A SVM-Pairwise System for Assessment of Allergenicity and Allergic Cross-Reactivity in Proteins

Multidimensional Mapping Method Using an Arrayed Sensing System for Cross-Reactivity Screening

Assessment of the Sensitizing Potential of Processed Peanut Proteins in Brown Norway Rats: Roasting Does Not Enhance Allergenicity

Physical Properties of Intact Proteins May Predict Allergenicity or Lack Thereof

Structural Differences between Human Proteins and Aero- and Microbial Allergens Define Allergenicity

TFPP: An SVM-Based Tool for Recognizing Flagellar Proteins in Trypanosoma brucei

FaaPred: A SVM-Based Prediction Method for Fungal Adhesins and Adhesin-Like Proteins

Allergenicity Assessment of Allium sativum Leaf Agglutinin, a Potential Candidate Protein for Developing Sap Sucking Insect Resistant Food Crops

Graph Based Study of Allergen Cross-Reactivity of Plant Lipid Transfer Proteins (LTPs) Using Microarray in a Multicenter Study

AllerHunter: A SVM-Pairwise System for Assessment of Allergenicity and Allergic Cross-Reactivity in Proteins

Similar Documents

AllerHunter: A SVM-Pairwise System for Assessment of Allergenicity and Allergic Cross-Reactivity in Proteins

Multidimensional Mapping Method Using an Arrayed Sensing System for Cross-Reactivity Screening

Assessment of the Sensitizing Potential of Processed Peanut Proteins in Brown Norway Rats: Roasting Does Not Enhance Allergenicity

Physical Properties of Intact Proteins May Predict Allergenicity or Lack Thereof

Structural Differences between Human Proteins and Aero- and Microbial Allergens Define Allergenicity

TFPP: An SVM-Based Tool for Recognizing Flagellar Proteins in Trypanosoma brucei

FaaPred: A SVM-Based Prediction Method for Fungal Adhesins and Adhesin-Like Proteins

Allergenicity Assessment of Allium sativum Leaf Agglutinin, a Potential Candidate Protein for Developing Sap Sucking Insect Resistant Food Crops

Graph Based Study of Allergen Cross-Reactivity of Plant Lipid Transfer Proteins (LTPs) Using Microarray in a Multicenter Study

AllerHunter: A SVM-Pairwise System for Assessment of Allergenicity and Allergic Cross-Reactivity in Proteins