**6. Epitope mapping model using IEDB**

The IEDB was first published in 2004 using data that limited numbers, text, and tables of scientific literature. Finally, in 2015, the IEDB experiments' number increased by 140% to exceed 1.6 million, and receptor sequence data in the IEDB scheme. Previously, this device could only capture antibodies and the T cell receptor (TCR) but can now capture antibodies and complementarity determining regions (CDR), which is essential for the antigen's specificity of its diversity. The scope of this device extends throughout the epitope for data relating to all species includes immunity body/antibody, the context of T cell binding, and MHC-related infections, allergies, autoimmune, and transplantation of certain diseases and features to access also summarize data in terms of quantity and complexity [20].

An antigenicity analysis is used, and epitope mapping is also carried out (**Figure 1**) to analyze areas that have antigenicity potential against B-cell, for example, using Bepipred and Emini methods. Both are done based on a database owned by IEDB (The Immune Epitope Database). Selection of epitopes according to the score above the threshold. Epitope mapping was performed using Bepipred software from the immune epitope database (HTTP://toolsiedb.ofg/bcell/) to find linear B cell epitopes from a sustainable region with an average threshold value of 0.030. This method is classically used to measure propensity.

Moreover, using hidden Markov programming [21], we show the epitope mapping of the OMP28 protein, a typhus vaccine candidate researched by Saxena et al. (2012). OMP28 is outer membrane protein 28 from *Salmonella enterica subsp. enterica* serovar Typhi with Accession number NCBI: ACX42427. The OMP28 protein sequence is MNKFSLATAGIIVAALVTSVSVN AATDTTKTNVTPKGMSCQEFVDLNPQTMAPVAFWVLNEDEDFKGGD

YVDFQETETTAVPLAVELCKKNPQSELSKIKDEIKKELSK. Preferably, before starting epitope mapping, we need to make sure that the sequence that will be

*In-Silico Approach in the Development of* Salmonella *Epitope Vaccine DOI: http://dx.doi.org/10.5772/intechopen.96313*

**Figure 1.** *Steps of epitope mapping.*

**Figure 2.** *B cell epitope mapping using the IEDB Bepipred method (IEDB.org) [19].*

analyzed is a conserved region. This step can be done by aligning many of the same protein sequences from different strains of *salmonella*.

The epitope mapping results are shown in **Figures 2** and **3**; the yellow area is considered to have high antigenicity potential. In bepipred linear epitope prediction, a value equal to or greater than the threshold value of 0.030 is said to have a strong potential to bind to B cells. This is also done for other methods, such as the emini surface method with a threshold limit of 1.

From the **Tables 1** and **2**, it can be seen that the highest epitope potential is in positions 62th–80th because it has the highest score 1.581 with a long sequence of 19 amino acid sequences, and 22–38 positions with a score of 1.449 along with



#### **Table 1.**

*Resume of Bepipred analysis on OMP28 sequence.*



#### **Table 2.**

*Resume of Emini analysis on OMP28 sequence.*

the 17 amino acid sequences. As a comparison, the antigenicity analysis was also performed using the emini surface technique, and the most significant potential was obtained at positions 25–34 with a sequence length of 10 amino acids, namely ATDDTKTNVT.

Based on the analysis of bepipred and emini surface, the sequences that have the potential to provide the greatest immunogenicity can be identified at positions 22–38 and positions 62–80. Furthermore, this peptide can be produced by the recombinant protein method. The multi-epitope candida vaccine is considered more promising than the single epitope vaccine.
