SubVis

SubVis visualizes and compares the effects of multiple amino acid substitution matrices on protein pairwise sequence alignments to analyze mutation patterns and alignment quality.

Key Features:

• Visual exploration of alignments: Produces visual representations that reveal high-level and residue-level alignment quality and specific amino acid substitutions.
• Multiple substitution matrix support: Accepts predefined and custom amino acid substitution matrices for comparative analysis.
• Matrix families included: Supports common substitution matrix families such as BLOSUM and PAM for direct comparison.
• Pairwise alignment comparison: Applies and compares multiple matrices on pairwise sequence alignments to evaluate differences in alignment outcomes.
• R alignment functions: Leverages alignment functions available in R for computation of sequence alignments.
• Simultaneous matrix application: Enables loading and simultaneous application of multiple matrices to streamline comparative analyses.
• Visualization generation: Generates visual outputs using JavaScript to represent alignment metrics and substitution patterns.

Scientific Applications:

• Mutation pattern analysis: Investigates patterns of amino acid substitution across protein sequences to inform evolutionary or functional studies.
• Alignment sensitivity assessment: Evaluates how choice of substitution matrix affects sequence similarity estimates and alignment quality.
• Matrix selection and hypothesis testing: Compares substitution strategies to select matrices that align with specific research hypotheses or datasets.
• Comparative substitution analysis: Assesses differences between substitution matrix families (e.g., BLOSUM vs PAM) on alignment outcomes.

Methodology:

Uses alignment functions available in R, loads predefined and custom substitution matrices, applies them to pairwise sequence alignments for comparison, and generates visualizations via JavaScript.