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OJBTM
Online Journal of Bioinformatics©
Prediction of epitopes for vaccine against Salmonella typhimurium.
*Vipin Ranga1, 2, *Sushil Kumar Shakyawar 1, 2, Utpal Bora2, Dinesh Kumar1, §
1Genes & Genetic Resources Molecular Analysis Lab, National Bureau of Animal Genetic Resources, Karnal-132 1001, Haryana, 2Department of Biotechnology, Indian Institute of Technology, Guwahati-781 039, Assam, INDIA. *Both contributed equally
ABSTRACT
Ranga V, Shakyawar SK, Bora U, Kumar D., Prediction of epitopes for vaccine against Salmonella typhimurium, Onl J Bioinform., 20(3): 221-232, 2019. Salmonella typhimurium send protein signals to intestinal cells which signal M cells into ingesting S typhymurium giving this bacteria access to the reticuloendothelial system. We attempt to predict putative surface epitopes against Human-MHC class-II genes with MHCPred software using the bacterial surface proteins gene sequences of Salmonella typhimurium. We found 257 surface membrane protein genes of Salmonella typhimurium LT2 as targets and extracted 230 essential genes (EG) from DEG database for conserved critical domains. By applying this method we avoided strategic antigen diversity often displayed by Salmonella to supress immune system of hosts. BLAST-P analysis of ST-EG against human genome revealed 13 non-human homologous membrane genes having targeted epitopes. VexiJen threshold was calculated to select 11 genes of which 10 had at least 3 putative epitopes subjected to in silico analysis for hydrophilicity and antigenicity to compute most efficient three epitopic regions of each gene. Cluster scores and surface confirmation by homology based 3-D protein modelling was used to identify the best linear surface epitope for vaccine. OJBTM
Key words: Antigenicity; homology
modelling; hydrophilicity; Membrane protein; NCBI Blastp.