AligNet

AligNet aligns protein-protein interaction networks (PPINs) to identify conserved topological and functional relationships across species or conditions.

Key Features:

• R package implementation: Provided as an R package for performing PPIN alignments.
• Parameter-free pairwise alignment: Executes pairwise PPIN alignments without user-defined parameters.
• Global pairwise alignments: Produces global alignments between pairs of networks.
• Integration of topology and biology: Integrates network topology (structural data) and biological/functional information in the alignment process.
• Biological meaningfulness: Generates alignments that conserve protein functions and biological relevance.
• Computational efficiency: Reports more efficient computation compared to state-of-the-art tools for large-scale PPINs.

Scientific Applications:

• Protein function prediction: Infers functions of newly discovered proteins by transferring annotations across aligned networks.
• Evolutionary studies: Identifies conserved pathways and evolutionary relationships by comparing interaction networks across species.
• Disease research: Detects altered interaction patterns and potential therapeutic targets by aligning disease and reference PPINs.

Methodology:

Performs global pairwise PPIN alignments using a parameter-free algorithm that integrates network topology (structural data) and biological/functional information.