Predicted philogeny, secondary conformational structure, and epitope antigenicity of immunological sequences in poultry

Abstract

Poultry production is faced with different types of stresses that are responsible for issues of animal welfare as well as for economic losses. Moreover, the immunity decreases when animals are stressed. In silico analyses are important in reducing the cost and in increasing the accuracy of scientific results. A bioinformatics tool was used to perform ontology studies on 15 different immunological sequences of poultry. The mRNA structures and sequences with maximum antigenic residues were also predicted. No homology was found between the sequences of poultry and mammals. These results helped in the prediction of new potential molecular markers. Of the 15 sequences that were analyzed, predictions could not be made for five because they were longer than 2500 nucleotides; for the remaining 10 sequences, 20 conformational structures per sequence were predicted and the most stable sequences were identified by their minimum free energy values. The highest antigenic epitopes were accepted by the maximum scores; 15 of the total 8934 epitopes that were predicted were analyzed. These results would aid future studies that use synthetic peptides or recombinants as markers or immunomodulators and would expand our understanding on how stress can modulate the immune system. These would also help in developing rapid diagnostic tools, in increasing animal welfare, biosecurity, and productivity, and also in developing of food additives and environmental enrichment for stress control, thereby, making animal production more sustainable.