Phylogenetic Analysis of HA Protein of Influenza A Virus Based on a Novel Alignment-Free Method

摘要

When a new subtype of HA gene is transmitted from aquatic birds to human, the influenza pandemics occur sometimes. Research of the origin and evolution of HA gene is an important task for biologists. In this study, based on an efficient mathematical method, a novel 3D graphical representation of protein sequence has been proposed to analyze HA protein of 351 strains of different viral subtype of influenza A virus. Then a mathematical descriptor was suggested to compute the distance between two different proteins which is very convenient for computation. And phylogenic tree without requiring multiple alignment was constructed based on the single linkage method. The evolutionary tree obtained is consistent with the previous studies. The results show that species virus host and geographical distribution possess vital effect on evolution routes of HA protein of influenza A virus.