Further evaluation of the utility of "Sliding Window" FASTA in predicting cross-reactivity with allergenic proteins

Regulatory Toxicology and Pharmacology

Volumn 54, Issue 3 SUPPL., 2009, Pages

  Cressman, Robert F ^a   Ladics, Gregory ^a  

^a DUPONT COMPANY   (United States)

Author keywords

Bioinformatics; FASTA; Local similarity; Protein allergenicity; Regulatory; Risk assessment

Indexed keywords

FOOD ALLERGEN;

ALGORITHM; ALLERGENICITY; AMINO ACID SEQUENCE; ARTICLE; BARLEY; CONTROLLED STUDY; CROSS REACTION; FOOD ALLERGY; INTERMETHOD COMPARISON; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEOMICS; RISK ASSESSMENT; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SOYBEAN; SPINACH; SUGAR BEET;

ALGORITHMS; ALLERGENS; COMPUTATIONAL BIOLOGY; CROPS, AGRICULTURAL; CROSS REACTIONS; DATABASES, PROTEIN; PLANT PROTEINS;

BETA VULGARIS SUBSP. VULGARIS; HORDEUM; LACTUCA; SPINACIA OLERACEA; ZEA MAYS;

EID: 67349234991     PISSN: 02732300     EISSN: 10960295     Source Type: Journal    
DOI: 10.1016/j.yrtph.2008.11.006     Document Type: Article

References (14)

1. Baxevanis A.D., and Ouellette B.F.F. Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins (1998), John Wiley & Sons, Inc., New York
2. Codex Alimentarius Commission, Alinorm 03/34: Joint FAO/WHO Food Standard Programme, Codex Alimentarius Commission, Twenty-Fifth Session, Rome, Italy, June 30-July 5, 2003. Appendix III, Guideline for the conduct of food safety assessment of foods derived from recombinant-DNA plants, and Appendix IV, Annex of the assessment of possible allergenicity, pp. 47-60.
3. FAO/WHO, 2001. Evaluation of allergenicity of genetically modified foods. Report of a Joint FAO/WHO Expert Consultation on Allergenicity of Foods Derived from Biotechnology, January 22-25, 2001, Rome, Italy.
4. Goodman R.E. Performing IgE serum testing due to bioinformatics matches in the allergenicity assessment of GM crops. Food and Chemical Toxicology 46 (2008) S24-S34
5. Hileman R.E., Silvanovich A., Goodman R.E., Rice E..A., Holleschak G., Astwood J.D., and Hefle S.L. Bioinformatic methods for allergenicity assessment using a comprehensive allergen database. Int. Arch. Allergy Immunol. 128 (2002) 280-291
6. Ladics G.S., Bannon G.A., Silvanovich A., and Cressman R.F. Comparison of conventional FASTA identity searches with the 80 amino acid sliding window FASTA search for the elucidation of potential identities to known allergens. Mol. Nutr. Food Res. 51 8 (2007) 985-998
7. Ladics G.S., Bardina L., Cressman R.F., Mattsson J.L., and Sampson H.A. Lack of cross-reactivity between the Bacillus thuringiensis derived protein Cry 1F in maize grain and dust mite Der p7 protein with human sera positive for Der p7-IgE. Regul. Toxicol. Pharmacol. 44 2 (2006) 136-143
8. Jenkins J.A., Griffiths-Jones S., Shewry P.R., Breiteneder H., and Mills E. Structural relatedness of plant food allergens with specific reference to cross-reactive allergens: an in silico analysis. J. Allergy Clin. Immunol. 115 (2005) 163-170
9. Pearson W.R., and Lipman D.J. Improved tools for biological comparison. Proc. Natl. Acad. Sci. USA 85 (1988) 2440-2448
10. Pearson W.R. Flexible sequence similarity searching with the FASTA3 program package. Methods Mol. Biol. 132 (2000) 185-219
11. Scheurer S., Son D.Y., Boehm M., Karamloo F., Franke S., Hoffmann A., Haustein D., and Veiths S. Cross-reactivity and epitope analysis of Pru a 1, the major cherry allergen. Mol. Immunol. 36 (1999) 155-167
12. Silvanovich A., Nemeth M.A., Song P., Herman R., Tagliani L., and Bannon G.A. The value of short amino acid sequence matches for prediction of protein allergenicity. Toxicol. Sci. 90 1 (2006) 252-258
13. Stadler M.B., and Stadler B.M. Allergenicity prediction by protein sequence. FASEB J. (2003) 1141-1143
14. Thomas, K., Bannon, G., Hefle, S., Herouet, C., Holsapple, M.P., Ladics, G.S., MacIntosh, S., Privalle, L., 2005. In: Silico Methods for Evaluating Human Allergenicity to Novel Proteins: International Bioinformatics Workshop Meeting Report-Mallorca, Spain, February 24, 25, 2005. Toxicol. Sci. 88 (2), 307-310.