Distributional Analysis Of Hemagglutinin Gene's SSRs Of Influenza A Virus

Simple sequence repeat (SSR) analysis and its application in bioimformatics and evolutionary studies are important issues for investigating the genome evolution, protein function and inter-action between genetics and environment. In some studies, many characteristics of SSRs are found in eukaryotes and prokaryotes:the distribution of SSRs in the genome was not random, the number of repetitions will vary for species; most, but not all, of SSRs are ubiquitous and abundant in a genome; SSRs are highly variable and unusually polymorphic and the flanking sequence are comparatively conserved; SSRs types are in accordance; and SSRs are thought to may influence transcriptional activity and to play a functional role in the evolution of gene regulation. The highly changeability of SSR was caused by the slipped-strand mispairing in DNA replication, recombination and repair. With the development of research, SSRs could be able to affect the Chromatin Structure, regulation on activity of gene, DNA recombination and its mismatch repair, and plays an important role in evolution process in organisms. Many scholars have made a lot of research on influenza virus in recent years, which covers in genomics, proteomics, epidemiology, etc., but no study of gene's SSRs of influenza A virus in different host has been reported as yet. We analyze the SSRs of influenza A virus'genome which based on the biological and statistical analysis, and explore the law of SSRs'distribution and the cause of changes of the distribution.Influenza is an infection caused by influenza (flu) viruses, which are type A members of the Orthomyxoviridae family, including IAV, IBV, ICV. Influenza which caused by IAV is the most harmful disease. This paper chose the influenza A viruses'genes coding for hemagglutinin as the object and caculated SSRs in genomes by using the method of biostatistical analysis. The results of SSRs in genomes show that the distribution of the hemagglutinin amino acid sequences of influenza A virus occur a certain regularity in SSRs. Although relative abundance and relative density exhibit very high similarity, which indicates that SSRs might be related to genomic point mutations. Some of these sequences show different preference for most common SSRs and longest SSRs. We infer that the hemagglutinin amino acid sequences of influenza A virus is in preference to the A-rich repeats. It inferred that longer repeats have higher mutation rates and hence are unstable, which could be environmental pressure and mutant stability lead to the frequency of SSRs decrease gradually with repeat length. It is reported that there is a similar case in diverse completed HIV-1 genomes. Our results show that all of them are virus, but there are a large number of SSRs especially mononucleotide repeats, which imply that mononucleotide repeats in hemagglutinin amino acid sequences are extremely active, and dinucleotide repeats were fewer of other SSR repeats, which evidence that the most common SSR motifs are different in various virus.