Local versus Global Biological Network Alignment

Biological network alignment (NA) aims to find regions of similarities between molecular networks of different species. There exist two categories of NA: local (LNA) and global (GNA). LNA aims to find small highly conserved network regions and produces many-to-many mapping between nodes of the compared networks, while GNA aims to find large conserved subgraphs and produces one-to-one node mapping. Given the different outputs of LNA and GNA, when a new NA method is proposed, it is compared against existing methods from the same category. However, both NA categories have the same goal: to allow for transferring functional knowledge from well-studied model species to poorly-studied species between conserved network regions. So, which one to choose, LNA or GNA? To answer this, we introduce the first systematic evaluation of the two NA categories, along with new measures of both topological and biological alignment quality that allow for fair comparison of the different LNA and GNA output types, as such measures have not been proposed to date.

Reference: Lei Meng, Aaron Striegel, Tijana Milenkovic. "Local versus Global Biological Network Alignment," Bioinformatics, 32(20): 3155-3164, 2016.

Contact: tmilenko [at] nd [dot] edu

Software: The executables and source code are available for download, along with detailed usage instructions.