Pandemrix vaccine induced narcolepsy was caused by molecular mimicry between the H1N1 influenza virus nucleoprotein and the human hyprocretin receptor. The BLASTP bioinformatics tool was used to determine a protein sequence alignment score between the influenza nucleoprotein and human hyprocretin receptor. This score was used as a baseline to assess autoantigen sequence alignment to vaccine antigens and contaminants. Significant protein sequence alignment was observed between autoantigens and vaccine antigens, contaminants, with numerous scores exceeding the baseline value.