It was reported that the allergenicity prediction based on similarities of protein motifs was superior to that based on amino acid sequence comparison (Stadler et al. FASEB J. 17, 1141, 2003). We therefore extracted 66 allergen motifs from 1,192 allergen sequences in ADFS with MEME motif discovery tool (ver. 3.5.0) and found that 142 allergen sequences did not match any of the allergen motifs. The motif-based method will predict your query protein allergenic when your query sequence: 1) matches an allergen motif with a normalized score (by pftool) greater than 8.5, or 2) is aligned to the 142 allergen sequences with a high similarity by BLAST algorithm (the default E-value, <10-3). It should be noted that the prediction results will not necessarily indicate that your query protein has an allergenicity.