Identifying Antimicrobial Peptides using Word Embedding with Deep Recurrent Neural Networks

Abstract

Antibiotic resistance constitutes a major public health crisis, and finding new sources of antimicrobial drugs is crucial to solving it. Bacteriocins, which are bacterially-produced antimicrobial peptide products, are candidates for broadening the available choices of an-timicrobials. However, the discovery of new bacteriocins by genomic mining is hampered by their sequences low complexity and high variance, which frustrates sequence similarity-based searches. Here we use word embeddings of protein sequences to represent bacteriocins, and apply a word embedding method that accounts for amino acid order in protein sequences,to predict novel bacteriocins from protein sequences without using sequence similarity. Our method predicts, with a high probability, six yet unknown putative bacteriocins in Lactobacil-lus. Generalized, the representation of sequences with word embeddings preserving sequence order information can be applied to protein classification problems for which sequence simi-larity cannot be used.