用邻位相连法方法确定HIV-1M组基因分型的最佳区域

Determine the best genotyping area of the HIV-1M group with NJ

目的为进一步确定HIV-1M组基因分型的最佳区域。方法从Genbank中筛选出对各成熟肽区域有注释来源,来自于不同国家地区的104条HIV-1M组全基因组序列。对序列的结构区域gag区、pol区、env区及env的亚区域gp41和gp120分别建邻位相连(NJ)系统进化树。结果 pol区未能把D亚型和B亚型分开;gag区未把K亚型和F亚型分开;env区能对HIV-1M组正确分型;env的亚区域gp41未能把K亚型与H和F亚型分开,J亚型未与A亚型分开。env的亚区域gp120未能把J亚型与A1亚型分开。结论用NJ系统进化树方法确定env区最能代表HIV-1M全基因组序列进行分型。

Objective To determine the best genotyping area of the HIV-IM group. Methods 104 complete genome sequences of HIV-1M group that had been given the annotation about every region and derived from different country were downloaded from Cenbank. Phylogenetic trees on gag region, pol region, env region,gp41 region and gpl20 region were established by neighbor-join- ing method. Results The env region was the best region instead of the complete genome sequence. Conclusion We have found that the best genotyping region of HIV-1M group was env region sequences using bioinformatics.