creators_name: Saha, Sudipto
creators_name: Raghava, G.P.S.
type: article
datestamp: 2012-01-09 04:22:01
lastmod: 2012-01-09 04:22:01
metadata_visibility: show
title: AlgPred: prediction of allergenic proteins and mapping of IgE epitopes.
ispublished: pub
subjects: QR
full_text_status: public
note: OPEN ACCESS
abstract: In this study a systematic attempt has been made to integrate various approaches in order to predict allergenic proteins with high accuracy. The dataset used for testing and training consists of 578 allergens and 700 non-allergens obtained from A. K. Bjorklund, D. Soeria-Atmadja, A. Zorzet, U. Hammerling and M. G. Gustafsson (2005) Bioinformatics, 21, 39-50. First, we developed methods based on support vector machine using amino acid and dipeptide composition and achieved an accuracy of 85.02 and 84.00%, respectively. Second, a motif-based method has been developed using MEME/MAST software that achieved sensitivity of 93.94 with 33.34% specificity. Third, a database of known IgE epitopes was searched and this predicted allergenic proteins with 17.47% sensitivity at specificity of 98.14%. Fourth, we predicted allergenic proteins by performing BLAST search against allergen representative peptides. Finally hybrid approaches have been developed, which combine two or more than two approaches. The performance of all these algorithms has been evaluated on an independent dataset of 323 allergens and on 101 725 non-allergens obtained from Swiss-Prot. A web server AlgPred has been developed for the predicting allergenic proteins and for mapping IgE epitopes on allergenic proteins (http://www.imtech.res.in/raghava/algpred/). AlgPred is available at www.imtech.res.in/raghava/algpred/.
date: 2006-07-01
date_type: published
publication: Nucleic acids research
volume: 34
number: Web Se
publisher: Oxford University Press
pagerange: W202-9
refereed: TRUE
issn: 1362-4962
official_url: http://nar.oxfordjournals.org/content/34/suppl_2/W202.full.pdf+html
related_url_url: http://www.imtech.res.in/raghava/algpred/
related_url_type: author
citation:   Saha, Sudipto and Raghava, G.P.S.  (2006) AlgPred: prediction of allergenic proteins and mapping of IgE epitopes.  Nucleic acids research, 34 (Web Se).  W202-9.  ISSN 1362-4962     
document_url: http://crdd.osdd.net/open/141/1/raghava2006.1.pdf