Sherry Dadgar


Estimating evolutionary conservation of cleavage site peptides among HA protein of all strains facilitates vaccine development against pandemic influenza. Conserved epitopes may be useful for diagnosis of animals infected with the influenza virus, and preventing their spread in other regions [ 1]. In the preliminary stage of this study, in silico analysis of hemagglutinin was applied to predict potential cleavage sites of each strain employing

SigCleave [2] and SignalP 3.0 server [3]. The second stage of the study focused on analyzing the structure of connecting peptides of hemagglutinin cleavage sites based on the availability of the existing experimental data. Our result divulges higher frequency of base amino acids, essential for processing by the cellular protease, among pathogenic strains compared with non/low pathogenic strains. In addition, two complementary methods for identifying conserved amino acids were applied: statistical entropy based method, possibly the most sensitive tool to estimate the diversity of peptides [5], and relative entropy estimation. Analysis of both methods demonstrates that the connecting peptide of HA cleavage site of AIV in the United States were highly conserved over long periods of time. Entropy values aid to select those sequences that have the highest potential for mutation in a broad spectrum of avian population. Position 340 among our group of strains with the entropy value of 0.877928 has the highest bit of information value where highly conserved positions are those with H

Library of Congress Subject Headings

Peptides--Analysis; Avian influenza A virus--United States--Research; Scission (Chemistry)

Publication Date


Document Type


Student Type


Degree Name

Bioinformatics (MS)


Gary R. Skuse

Advisor/Committee Member

Michael V. Osier

Advisor/Committee Member

Carol Marchetti


Physical copy available from RIT's Wallace Library at QP552.P4 D34 2008


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