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The SMAL web server: global multiple network alignment from pairwise alignments.

Jakob Dohrmann1, Rahul Singh2

  • 1Department of Computer Science, San Francisco State University, San Francisco, CA 94132, USA.

Bioinformatics (Oxford, England)
|July 6, 2016
PubMed
Summary
This summary is machine-generated.

Multiple network alignment (MNA) is computationally challenging. SMAL (Scaffold-Based Multiple Network Aligner) is a new tool that rapidly generates superior MNAs from pairwise network alignments, enabling easier analysis and modification.

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Area of Science:

  • Computational biology
  • Bioinformatics
  • Systems biology

Background:

  • Protein-protein interaction networks (PPINs) are crucial for understanding protein function, evolutionary relationships, and interactome conservation.
  • Multiple network alignment (MNA) is computationally intensive, with limited available tools and functionalities, hindering comparative interactome analysis.

Purpose of the Study:

  • To address the computational complexity and limitations of existing MNA algorithms.
  • To develop a user-friendly and efficient tool for generating and manipulating multiple network alignments.

Main Methods:

  • SMAL (Scaffold-Based Multiple Network Aligner), a public, open-source, web-based application, was developed.
  • SMAL combines existing pairwise network alignments (PNAs) to rapidly generate MNAs.
  • The tool supports visualization and interactive data exploration, allowing for persistent alignments that can be modified by adding new networks without re-computation.

Main Results:

  • SMAL successfully generates MNAs by combining PNAs, overcoming the computational challenges of existing methods.
  • The SMAL application provides visualization and interactive features for enhanced data analysis and sensemaking.
  • Comparative studies show SMAL MNAs are superior in identifying homologs and interologs, with a higher fraction of functionally similar correspondences to the scaffold network.

Conclusions:

  • SMAL offers a significant advancement in MNA, providing a rapid, flexible, and superior method for analyzing biological networks.
  • The tool's persistence and modification capabilities facilitate iterative analysis and integration of new data.
  • SMAL is a versatile network alignment tool applicable to PPINs and other arbitrary networks.