Shigella flexneri outer membrane protein A (OmpA) has good immunogenicity for application

prospect in vaccine development. In this paper, phylogenetic analysis found that Shigella flexneri and enteric

bacterium relationship was higher than others by MEGA. By online software, the prediction results showed that OmpA protein is a hydrophilic and secreted protein, exists multiple restriction enzyme sites. Using TMHMM Server v.2.0 software predicted that OmpA has not transmembrane structure and locats outside cell membrane. OmpA secondary structure contains random coil helix 41.09 %, alpha helix 26.44 %, beta turn 10.06 %, extended strand 22.41 % by SOPMA method, respectively. Using the SignalP 4.1 software analysis showed that the 1-21 amino acids of OmpA are signal peptide sequence. The 3D structure prediction found that OmpA protein is barrel structure by Swiss-Model program. Using ABCpred and BepiPred prediction program, OmpA has 3 B cell epitopes. By the prediction method of quantitative matrix and artificinal neural network, OmpA protein has 1 CTL epitopes. OmpA protein has 1 Th epitopes using an online server prediction for MHC class Ⅱ peptide binding affinity. OmpA recombinant epitope peptide is designed with better immunogenicity. This paper would lay a foundation for the study of OmpA multiepitope tandem vaccine.