SMAL

SMAL constructs multiple network alignments (MNAs) from existing pairwise alignments (PNAs) to align protein-protein interaction networks (PPINs) for protein function prediction, conserved interactome analysis, and evolutionary correspondence mapping.

Key Features:

• Scaffold-Based Alignment: Constructs MNAs by assembling existing PNAs around a chosen scaffold PPIN to anchor correspondences across networks.
• Reference Scaffold Selection: Allows selection of a specific PPIN as the reference scaffold to define alignment targets relative to that network.
• Persistent Alignments: Preserves established MNAs and enables incremental addition of new networks without full re-computation of the alignment.
• Performance on Homologs and Interologs: Produces MNAs that identify a higher total number of homologs and interologs and maintain a greater fraction of functionally similar or homologous correspondences relative to the scaffold network.
• Generic Network Alignment Capability: Applies the scaffold-based approach to arbitrary networks beyond PPINs.

Scientific Applications:

• Functional Prediction: Infers protein function by transferring annotations across aligned nodes in PPINs based on conserved correspondences.
• Conservation Studies: Detects conserved interactome elements across species or conditions by comparing MNAs anchored on a scaffold PPIN.
• Evolutionary Analysis: Maps evolutionary correspondences between networks to study conservation of interactions and homologous relationships.

Methodology:

SMAL assembles MNAs from existing pairwise network alignments (PNAs) using a scaffold-based approach anchored on a selected PPIN and supports incremental integration of new networks without recomputing the entire alignment.