Computational protocol: Parental LTRs Are Important in a Construct of a Stable and Efficient Replication-Competent Infectious Molecular Clone of HIV-1 CRF08_BC

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Protocol publication

[…] The proviral genomes of both the parental isolate and the infectious clone pBRGX were sequenced using a primer-walking protocol and the Sanger dideoxynucleotide chemistry, with three-fold coverage and complementary reads. These sequencing ladders were assembled with the Seqman Pro software, as described previously . Nucleotide and amino acid sequences were aligned with CLUSTAL and BLAST software. These whole genome sequences were annotated and deposited into GenBank (accession numbers JF719819 and JF719818, respectively).Genome sequence recombination analysis was performed using the Recombinant Identification Program (RIP 3.0), available from the Los Alamos HIV sequence database ( Phylogenetic analysis and trees were generated using a neighbor-joining method implemented in MEGA 5 (Molecular Evolutionary Genetics Analysis) , with 1000 bootstrap replicates. The evolutionary distances were computed using the Maximum Composite Likelihood method . Reference HIV-1 genome sequences of subtypes B, C, 07BC and 08BC were obtained from the Los Alamos HIV sequence database ( […]

Pipeline specifications

Software tools DNASTAR Molecular Biology Suite, MEGA
Application Phylogenetics
Organisms Human immunodeficiency virus 1, Escherichia coli, Human poliovirus 1 Mahoney
Diseases HIV Infections