Similar protocols

Pipeline publication

[…] ded from the analysis. A total of 6 out of 667 (0.88%) sequences were found to be hypermutated., During the preliminary analysis of viral quasispecies a link was identified between sequences of subjects OI and OK. We ruled out a potential contamination by (1) similar clustering patterns observed in structural genes, env and gag, of the same subjects (env/gag unpublished data from same cohort); (2) similar branching topology of viral sequences obtained at multiple timepoints of sampling; (3) nucleic acid isolation, PCR amplification and sequencing were separated by place and time; and (4) proper quality controls were used in each experiment., Nucleotide sequences were codon aligned using the MUSCLE algorithm implemented in Mega 5 followed by manual adjustment in Bioedit . For HIV-1 subtyping, three sequences per patient were randomly selected from the pool of generated viral quasispecies. The selection criteria included earliest timepoint available and sequence length with more than 90% coverage of the targeted region (5,041 to 6,310 nt position in HXB2). To determine phylogenetic relationships and clustering patterns of generated viral sequences, the phylogenetic tree reconstruction was performed using Neighbor joining, Maximum likelihood, and Bayesian methods. A standard set of HIV-1 subtype references from LANL was included in the analysis. The sequence CPZ.CM.98.CAM3.AF115393 was used as an outgroup. The online Rega-2 subtyping tool was used in […]

Pipeline specifications

Software tools MUSCLE, MEGA, BioEdit