PANADA

PANADA generates protein similarity networks from pairwise sequence and structural homology to support functional inference and network-based analysis in Cytoscape.

Key Features:

• Network construction: Builds protein similarity networks using pairwise sequence or structural alignments across protein sets or via database search from a single query sequence.
• Cytoscape integration and visualization: Exports networks to Cytoscape for visualization and analysis to assess transferability of functional inference across proteins.

Scientific Applications:

• Functional annotation: Supports transfer of functional annotations by revealing homologous relationships derived from sequence and structural similarity networks.
• Comparative network analysis: Enables identification of potential functional similarities and differences among proteins via network visualization to inform hypothesis generation and experimental design.

Methodology:

Constructs similarity networks from pairwise sequence and structural comparisons, including database searches from single sequences, and exports networks for visualization in Cytoscape.