Available at: http://www.codexalimentarius.net/download/standards/10021/CXG_045e
This document recommends the following sequence comparisons between transgenic and allergenic proteins:
8. The purpose of a sequence homology comparison is to assess the extent to which a newly expressed protein is similar in structure to a known allergen. This information may suggest whether that protein has an allergenic potential. Sequence homology searches comparing the structure of all newly expressed proteins with all known allergens should be done. Searches should be conducted using various algorithms such as FASTA or BLASTP to predict overall structural similarities. Strategies such as stepwise contiguous identical amino acid segment searches may also be performed for identifying sequences that may represent linear epitopes. The size of the contiguous amino acid search should be based on a scientifically justified rationale in order to minimize the potential for false negative or false positive results*. Validated search and evaluation procedures should be used in order to produce biologically meaningful results.
9. IgE cross-reactivity between the newly expressed protein and a known allergen should be considered a possibility when there is more than 35% identity in a segment of 80 or more amino acids (FAO/WHO 2001) or other scientifically justified criteria. All the information resulting from the sequence homology comparison between the newly expressed protein and known allergens should be reported to allow a case-by-case scientifically based evaluation.
* It is recognized that the 2001 FAO/WHO consultation suggested moving from 8 to 6 identical amino acid segments in searches. The smaller the peptide sequence used in the stepwise comparison, the greater the likelihood of identifying false positives, inversely, the larger the peptide sequence used, the greater the likelihood of false negatives, thereby reducing the utility of the comparison.