Regulatory toxicology and pharmacology : RTP
-
Regul. Toxicol. Pharmacol. · Aug 2009
Further evaluation of the utility of "sliding window" FASTA in predicting cross-reactivity with allergenic proteins.
FAO/WHO has recommended that IgE cross-reactivity between a transgenic protein and allergen be considered when there is greater than 35% identity over a sliding "window" of 80 amino acids. In a previous work, we evaluated the false positive and negative rates observed using the FAO/WHO criteria versus conventional, whole protein FASTA analyses [Ladics, G. S., Bannon, G. ⋯ Examination of the matches not recognized by the conventional search revealed two scenarios: (1) "true" false positives consisting of low statistical significance (as measured by E score, i.e., a measure of the potential random occurrence of aligned sequences used to evaluate the significance of an observed alignment) alignments not contained in the conventional FASTA outputs, and (2) above-threshold sliding window alignments that fell below the 35% identity threshold with the conventional FASTA analysis. Although some alignments within this second group were between regions of low sequence complexity, where there was little/no change in E score, the majority of the alignments displayed more significance (lower E scores) under the conventional FASTA algorithm, yet did not meet the threshold defined by FAO/WHO. These data question the utility of the FAO/WHO recommended sliding window FASTA compared to the traditional whole sequence FASTA analysis coupled with appropriate statistical analysis.