Abstract
BackgroundThe alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Network alignment can be used to transfer biological knowledge between species. Although different PPI-network alignment algorithms were introduced during the last decade, developing an accurate and scalable algorithm that can find alignments with high biological and structural similarities among PPI networks is still challenging.ResultsIn this paper, we introduce a new global network alignment algorithm for PPI networks called PROPER. Compared to other global network alignment methods, our algorithm shows higher accuracy and speed over real PPI datasets and synthetic networks. We show that the PROPER algorithm can detect large portions of conserved biological pathways between species. Also, using a simple parsimonious evolutionary model, we explain why PROPER performs well based on several different comparison criteria.ConclusionsWe highlight that PROPER has high potential in further applications such as detecting biological pathways, finding protein complexes and PPI prediction. The PROPER algorithm is available at http://proper.epfl.ch.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1395-9) contains supplementary material, which is available to authorized users.
Highlights
The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems
We introduce a new measure for evaluating the performance of algorithms in aligning biological pathways between species
In order to evaluate the performance of algorithms in aligning biological pathways, we introduce a new measure
Summary
The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Proteins are large biomolecules that carry out vital functions in living cells. They typically carry out these functions in concert with other biomolecules, especially other proteins, which enables their diverse functionality, such as forming signaling networks and metabolic pathways, and regulating enzymatic activities [1]. In this context, the term protein-protein interaction (PPI) stands for the mutual interactions between pairs of proteins.
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