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Chapter 10 : Bioinformatics for Predicting Allergenicity

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Bioinformatics for Predicting Allergenicity, Page 1 of 2

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Abstract:

The ability of a food or a food protein to cause allergic sensitization and to elicit an allergic reaction is the result of a complex set of interactions involving both the immune and digestive systems. It may be possible to infer potential allergenicity by comparing a protein of interest to known allergenic proteins. One major tool for conducting such a comparison is bioinformatic analysis. Bioinformatics can be used to compare primary sequences, secondary and tertiary structures, functional classifications, and evolutionary relationships for entire proteins or for domains within proteins. The utility of these comparisons depends on the availability of both appropriate data sources and analytical tools. Just as chemical or biological analyses should use characterized reagents and validated methods, bioinformatic analyses should be conducted using characterized databases and validated algorithms. Although a number of allergy-related databases are available, they are very different in design and content and in the degree to which information characterizing the content of the database is made available to users. A similar diversity exists among the available analytical resources for assessing potential allergenicity, and no standards or procedures have been developed for validating these resources. To illustrate the extent of the diversity among allergen-related bioinformatic resources, representative online allergen databases and analytical resources are described below. Based on the descriptive information available for each of these resources, principles of good database practice (GDP) can be developed that will maximize the utility of these resources.

Citation: Gendel S. 2006. Bioinformatics for Predicting Allergenicity, p 249-256. In Maleki S, Burks A, Helm R (ed), Food Allergy. ASM Press, Washington, DC. doi: 10.1128/9781555815721.ch10

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Amino Acids
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Food Safety
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References

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1. Brusic, V.,, M. Millot,, N. Petrovsky,, S. Gendel,, O. Gigonzac, and, S. Stelman. 2003. Allergen databases. Allergy 58:10931100.
2. Food and Agriculture Organization of the United Nations/World Health Organization. 2001. Evaluation of Allergenicity of Genetically Modified Foods: Report of a Joint FAO/WHO Consultation on Food Derived from Biotechnology. Food and Agriculture Organization of the United Nations, Rome, Italy.
3. Gendel, S. 1998. Sequence databases for assessing the potential allergenicity of proteins used in transgenic foods. Adv. Food Nutr. Res. 42:6392.
4. Gendel, S. 2002. Sequence analysis for assessing potential allergenicity. Ann. N.Y. Acad. Sci. 964:8798.
5. Hileman, R. A. Silvanovich,, R. Goodman,, E. Rice,, G. Holleschak,, J. Astwood, and, S. Hefle. 2002. Bioinformatic methods for allergenicity assessment using a comprehensive allergen database. Int. Arch. Allergy Immunol. 128:280291.
6. Ivanciuc,, O.,, C. Schein, and, W. Braun. 2003. SDAP: database and computational tools for allergenic proteins. Nucleic Acids Res. 31:359362.
7. Mari, A., and, D. Riccioli. 2004. The Allergome web site—a database of allergenic molecules. Aim, structure and data of a web-based resource. J. Allergy Clin. Immunol. 113:S301.
8. Poulsen, L. 2005. In search of a new paradigm: mechanisms of sensitization and elicitation of food allergy. Allergy 60:549558.
9. Sampson, H. 2004. Update on food allergy. J. Allergy Clin. Immunol. 113:805819.

Tables

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Table 1.

Online molecular databases

Citation: Gendel S. 2006. Bioinformatics for Predicting Allergenicity, p 249-256. In Maleki S, Burks A, Helm R (ed), Food Allergy. ASM Press, Washington, DC. doi: 10.1128/9781555815721.ch10
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Table 2.

Online allergy databases

Citation: Gendel S. 2006. Bioinformatics for Predicting Allergenicity, p 249-256. In Maleki S, Burks A, Helm R (ed), Food Allergy. ASM Press, Washington, DC. doi: 10.1128/9781555815721.ch10
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Table 3.

Allergenicity assessment Web sites

Citation: Gendel S. 2006. Bioinformatics for Predicting Allergenicity, p 249-256. In Maleki S, Burks A, Helm R (ed), Food Allergy. ASM Press, Washington, DC. doi: 10.1128/9781555815721.ch10
Generic image for table
Table 4.

Characterization of allergen databases

Citation: Gendel S. 2006. Bioinformatics for Predicting Allergenicity, p 249-256. In Maleki S, Burks A, Helm R (ed), Food Allergy. ASM Press, Washington, DC. doi: 10.1128/9781555815721.ch10
Generic image for table
Table 5.

Allergen analysis resources

Citation: Gendel S. 2006. Bioinformatics for Predicting Allergenicity, p 249-256. In Maleki S, Burks A, Helm R (ed), Food Allergy. ASM Press, Washington, DC. doi: 10.1128/9781555815721.ch10

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