Prediction of MHC Binding Peptides and Antigenic Peptides from Ascaris lumbricoides

Sonu Mishra and Virendra S Gom

Abstract

The parasitic disease Acariasis is the major concern because of its morbidity and mortality issue. In this investigation, we predicted the binding peptides of the MHC class I and MHC class II by Position Specific Scoring Matrices (PSSM) and Support Vector Machine (SVM) algorithms. We predicted the binding affinity of Cytochrome c oxidase subunit 2 (mitochondrion) having a 232 amino acids long residue sequence, which shows 224 nonamers. We predicted the peptide binding affinity to MHC I moles are as 8mer_H2_Db(The binding thresholds: 33.04,optimal score:52.494), 9mer_H2_Db(Optimal Score: 50.232, Binding Threshold: 17.96),10mer_H2_Db (The Optimal Score: 58.858, Binding Threshold: 41.32), 11mer_H2_Db(Optimal Score: 79.495, Binding Threshold: 56.96) and MHC- II molecules are as I_Ab.p, I_Ad.p, I_Ag7. We also study integrates prediction of peptide MHC class I binding; proteasomal C terminal cleavage and TAP transport efficiency by using sequence and properties of the amino acids. We also found the binding of peptides to different alleles by using Position Specific Scoring Matrix. PSSM based server will predict the peptide binders of Cytochrome c oxidase subunit 2 from Ascaris lumbricoides sequence to, which are found antigenic epitopes region in protein.