AlignmentViewer

AlignmentViewer visualizes and analyzes multiple sequence alignments (MSAs) to examine conservation, sequence-space distributions, and evolutionary constraints within protein families.

Key Features:

• Flexible visualization: Visualizes MSAs at multiple scales, from detailed views of specific regions to whole-alignment overviews.
• Conservation analysis: Computes and highlights conservation patterns across sequences to identify residues relevant to protein function or structure.
• Sequence-space distribution analysis: Analyzes sequence-space distributions to aid interpretation of evolutionary relationships and functional constraints.
• Database integration: Integrates MSAs with protein family databases and resources such as EVcouplings.org.
• Scalability: Handles large protein-family datasets, including alignments comprising tens of thousands of sequences.

Scientific Applications:

• Evolutionary coupling analysis: Supports workflows for evolutionary coupling analysis to predict residue-residue interactions, including integration with EVcouplings.org.
• Protein 3D structure preparation: Provides conservation and sequence-distribution information to inform computational modeling and structure prediction.
• Detection of functionally constrained interactions: Identifies conserved regions and residue patterns indicative of functionally constrained interactions and evolutionary pressure.

Methodology:

Performs visualization and analysis of MSAs, computes conservation patterns and sequence-space distributions, and integrates with protein family databases and resources such as EVcouplings.org.