To construct the protein dataset of H. pylori for antigen screening, available sequences were collected from the following public protein databases. (1) Protegen database (Yang et al. 2011) for protective antigens. (2) AntigenDB database (Ansari et al. 2010) for antigen proteins, which have been validated experimentally. (3) OMPdb database (Tsirigos et al. 2011) for β-barrel outer membrane proteins from Gram-negative bacteria. (4) PSORTdb database (Rey et al. 2005) for secreted proteins and outer membrane proteins of H. pylori. There is a total number of 14,702 protein sequences for H. pylori. And the sequence redundancy was reduced using CD-HIT (Fu et al. 2012) by selecting the representative sequence for sequences with identity above 90%. In the end, a non-redundant protein dataset of 381 sequences were constructed for H. pylori.

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