Protein conformational changes drive many biological processes. Few are as dramatic in terms of the structural changes that occur, or the biological consequences they produce, as those governing the formation of amyloid fibers. These highly ordered, beta-sheet rich structures were initially linked to several neurodegenerative disorders such as Alzheimer's disease, but more recently they have also been linked to normal biological functions such as cell adhesion and skin pigmentation. Prions represent a unique class of amyloid-forming proteins capable of switching to self-perpetuating conformations that are infectious and can be transmitted between different organisms. Several prions in the yeast S. cerevisiae have been identified, including Sup35, a protein involved in translation termination. Utilizing variants of this protein we find that several outstanding questions related to prion biology and the formation of amyloids can be investigated using arrays of short, surface-bound peptides. In this presentation I will discuss the use of peptide arrays to identify small elements of amino-acid sequence within several prions that govern their self-recognition and conformational conversion. Remarkably, we find that these same recognition sequences also govern the ability of the prions to adopt not just one amyloid conformation, but a suite of related yet structurally distinct conformations, known as prion strains. Further, our results suggest a mechanism that explains the previously perplexing relationship between the abilities of prions to form specific amyloid conformations and to cross species barriers. In the future, peptide arrays may enable the rapid analysis of the conformational conversion and assembly of other amyloid-forming proteins.