Computational protocol: Subtype Classification of Iranian HIV-1 Sequences Registered in the HIV Databases, 2006-2013

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Protocol publication

[…] A secondary analysis was performed using all Iranian HIV sequences from subtyping studies with pol, gag, env and full-length HIV-1 genome sequences registered in the HIV databases at the Los Alamos National Laboratory (www.hiv.lanl.gov) between 2006 and 2013. The sequences were downloaded along with reference nucleotide sequences for those regions [accession numbers: AB703607-AB703616, AY693842-AY693971, DQ077824-DQ077851, DQ077854-DQ077871, DQ115645-DQ115707, DQ149128-DQ149133, DQ788541-DQ788560, EU881931, FJ178375, FJ178376, FJ392730-FJ392755, FJ790242, FJ807629, FJ807630, GQ243705-GQ243708, GQ273945-GQ273960, GQ274861-GQ274878, GQ853425-GQ853428, GU724804-GU724845, HQ233645, HQ735066, HQ735068, KF029508-KF029592, EF158040- EF158043, GQ477442-GQ477451, DQ676872, AB253421, AB253429, AF286238, GU201516, AF286237, K03455, AY523387, AY173951, AY331295, U52953, U46016, AF067155, AY772699, K03454, AY371157, AY253311, U88824, AF077336, AF005494, AF075703, AJ249238, AY371158, AJ249236, AJ249237, AF377956, AF084936, AF061641, U88826, AY612637, AF190127, AF190128, AF005496, FJ711703, EF614151, GU237072, AF082394, AJ249239, GQ477441, GU564221, U54771, AY271690, AB485636, L39106, AF193276, AF049337, AF119819, AF119820, AF076998, AF193253, AY227107, AF064699, AY535659, AB286851, EF368372, EF368370, AF286230, HM067748, AY008715, AJ866553, AY093605, AY093603, AY093607, AF289548-AF289550, AF492623, AF492624, AF408629, AF408630, AF385936, DQ845388, AF450096, AF450097, DQ354120, AF516184, AY945736, AF286239, EU581825, EU581827, EU581828, AF377959, AY586541, AY894993, AY588971, AY588970, AY894994, AY586545, AY945737, AF457051, AF457072, AY371159, GQ229529, AY900571, AY900572, AY900574, AY900575, AJ670526, EU693240, EU697906, EU697908, FM877780, FM877782, FM877777, AJ404325, AM851091, DQ085872, DQ085873, DQ085874, DQ085876, AY771590, DQ085871, EF091932, AY727526, AY727527, AY535660, AB547464, DQ366659, DQ366662, EF165541, EF158043, EF158040, EF158041, EF087995, EF087994, EF116594, AF377957, FJ213781, FJ213782, FJ213780, EU735534, EU735536, EU735535, EU735538, EU735540, EU735339, EU170155, EU697904, EU697907, EU697909, FJ358521, FN392874, FN392876, FN392877, DQ358801, DQ358802, HM026456, GQ372987, FJ670529, HQ385477, HQ385479, HQ385478, L20587, L20571, AY169812, AJ302647, AY532635, AJ006022, AJ271370, HQ179987, GU111555, U42720, DQ373066, AF103818]. Pol, gag and env genes have been shown to be reliable regions for HIV-1 subtyping. , – Nucleotide sequences from each gene were aligned with the reference sequences using CLUSTAL W software. Phylogenetic trees were constructed using Neighbor-Joining (NJ) and Maximum Parsimony methods (1000 times bootstrap replicates) with Molecular Evolutionary Genetics Analysis (MEGA) software version 5. The Kimura 2-parameter model was used with a transition/transversion ratio of 1.5 and statistical support of the tree structures was obtained with 1000 bootstrap replicates. Significance was based on bootstrap values of >70%. To confirm the results obtained using MEGA5, sequences were re-analyzed using REGA. To improve the accuracy of the characterization of recombinant forms, Maximum Likelihood and NJ trees were re-constructed using RDP v.4.35 software. Results from all the different analyses were compared to determine the final subtype characterizations. […]

Pipeline specifications

Software tools Clustal W, MEGA
Databases HIV databases
Application Phylogenetics
Organisms Human immunodeficiency virus 1, Human immunodeficiency virus 2, Homo sapiens
Diseases Acquired Immunodeficiency Syndrome, HIV Infections