DomainViz

DomainViz identifies and visualizes protein domains across multiple sequences to analyze domain conservation for functional annotation and evolutionary studies.

Key Features:

• Monument valley plots (mv-plots): Generates mv-plots that display domain conservation along the dimensions of positionality and frequency of occurrence within input protein sequences.
• Domain-ordering figures: Produces conventional domain-ordering figures that illustrate the arrangement and conservation of domains within protein sequences.
• Integration with Pfam and Prosite: Leverages domain predictions from Pfam and Prosite for domain annotation.
• High-throughput domain searches: Performs high-throughput domain searches across multiple proteins and groups to assess conservation.
• Cross-family and cross-species analysis: Compares domain conservation within and between protein families and across species.

Scientific Applications:

• Evolutionary analysis: Facilitates inference of evolutionary patterns based on domain conservation across proteins.
• Functional annotation: Supports functional annotation of proteins through identification and mapping of domains.
• Comparative domain analysis: Enables comparison of domain arrangements and conservation across protein families and species.
• Interpretation of conservation metrics: Aids interpretation of positionality and frequency patterns of domains across input sequences.

Methodology:

Uses domain predictions from Pfam and Prosite, performs high-throughput domain searches, and generates monument valley plots (mv-plots) and conventional domain-ordering figures to represent positionality and frequency of domain occurrence.