Computational protocol: Community-Based HIV-1 Early Diagnosis and Risk Behavior Analysis of Men Having Sex with Men in Hong Kong

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Protocol publication

[…] To eliminate potential contamination, all of the obtained sequences were first subjected to an HIV-1 Blast search to compare these sequences with related reference sequences in the HIV Databases, which are funded by the Division of AIDS of the National Institute of Allergy and Infectious Diseases (NIAID), a part of the National Institutes of Health (NIH) (http://hiv-web.lanl.gov/content/index). Nucleotide sequences were aligned with the references using the ClustalX 1.81 program and further adjusted manually[]. The genetic distances of the analyzed HIV-1 sequences were calculated using Kimura’s two parameter model []. Phylogenetic trees were generated using the neighbor-joining method as implemented in the ClustalX 1.81 program. The branch significance was analyzed by bootstrap with 1,000 replicates. The trees were printed using the TreeView program[]. [...] Pearson’s x 2 test and Fisher’s exact test were performed to investigate the differences in the demographic data. All statistical analyses were performed using the software IBM SPSS Statistics 19. A p value equal to 0.05 was considered significant, and Bonferroni adjustments were made when conducting multiple comparisons. Multivariate logistic regression analysis was conducted using risk factors that had significant differences according to Pearson’s x 2 test or Fisher’s exact test. […]

Pipeline specifications

Software tools HIV-1 Blast Search, Clustal W, TreeViewX, SPSS
Databases HIV databases
Applications Miscellaneous, Phylogenetics, Nucleotide sequence alignment
Organisms Human immunodeficiency virus 1, Homo sapiens, Human immunodeficiency virus 2
Diseases Encephalitis, Arbovirus, Infection, HIV Infections