SimPlot

SimPlot analyzes recombination in HIV-1 genomes to identify recombination breakpoints and assess sequence conservation relevant to viral diversity, cytotoxic T lymphocyte (CTL) epitope variation, and vaccine research.

Key Features:

• Recombination Analysis: Identifies recombination events and breakpoints in aligned viral sequences, detecting mosaic HIV-1 subtypes including subtype C and across regions such as env, nef, and the 3' long terminal repeat.
• Sequence Comparison and Phylogenetic Bootstrapping: Performs sequence comparisons using maximal chi-squared analysis and phylogenetic bootstrapping to validate recombination breakpoints and phylogenetic relationships.
• Epitope Analysis: Assesses preservation or variation of known cytotoxic T lymphocyte (CTL) epitopes by comparing sequences to reference strains such as HIV-1LAI.
• Statistical Significance Testing: Evaluates statistical significance of nonconservative substitutions and other sequence differences across proteins including Env, Gag, Pol, and Nef.

Scientific Applications:

• Characterization of Viral Genomes: Supports cloning and sequencing analyses of virtually full-length genomes from seroconverters to characterize diverse HIV-1 subtypes and recombinant forms.
• Vaccine Development: Identifies conserved and variable CTL epitopes to inform antigen selection and assays of vaccine responsiveness, including comparisons to reference strains like HIV-1LAI.
• Epidemiological Studies: Analyzes sequence variation and recombination patterns across geographic regions, for example subtype C variants prevalent in India, to inform distribution and evolution of HIV-1 subtypes.

Methodology:

Aligns viral sequences and identifies recombination breakpoints by comparative analysis, applies maximal chi-squared analysis and phylogenetic bootstrapping to validate breakpoints, performs statistical tests for nonconservative substitutions, and assesses sequence conservation across known CTL epitopes.