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. 2006 Jul 1;34(Web Server issue):W202-9.
doi: 10.1093/nar/gkl343.

AlgPred: prediction of allergenic proteins and mapping of IgE epitopes

Sudipto Saha  1 , G P S Raghava
Affiliations

AlgPred: prediction of allergenic proteins and mapping of IgE epitopes

Sudipto Saha et al. Nucleic Acids Res. .

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/.

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Figures

Figure 1
Figure 1
The ROC plot of SVM-based method using amino acid (SVMcomp) and dipeptide (SVMdipep) composition.
Figure 2
Figure 2
(a) Snapshot of home page of AlgPred server (b) Snapshot of input page of AlgPred server. (c) Snapshot of output results.
See this image and copyright information in PMC

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References

    1. Sadok Y. Diagnosis of type I hypersensitivity by laboratory test. Tunis Med. 2005;83:441–444. - PubMed
    1. Scheurer S., Son D.Y., Boehm M., Karamloo F., Franke S., Hoffmann A., Haustein D., Vieths S. Cross-reactivity and epitope analysis of Pru a 1, the major cherry allergen. Mol. Immunol. 1999;36:155–167. - PubMed
    1. Santos A.B., Chapman M.D., Aalberse R.C., Vailes L.D., Ferriani V.P., Oliver C., Rizzo M.C., Naspitz C.K., Arruda L.K. Cockroach allergens and asthma in Brazil: identification of tropomyosin as a major allergen with potential cross-reactivity with mite and shrimp allergens. J. Allergy Clin. Immunol. 1999;104:329–337. - PubMed
    1. Broadfield E., McKeever T.M., Scrivener S., Venn A., Lewis S.A., Britton J. Increase in the prevalence of allergen skin sensitization in successive birth cohorts. J. Allergy Clin. Immunol. 2002;109:969–974. - PubMed
    1. Goodman R.E., Hefle S.L., Taylor S.L., Ree R.V. Assessing genetically modified crops to minimize the risk of increased food allergy: a review. Int. Arch. Allergy Immunol. 2005;137:153–166. - PubMed

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