Survey of biological network alignment: cross-species analysis of conserved systems

Comparative analysis of PPI networks between species is a significant step for predicting evolutionary conserved components or sub-structures in a system level. Network alignment is a computational technique to map similar components between networks. Aligning genome-wide PPI networks maps functionally similar nodes and edges and identifies conserved interactions or conserved modules. Existing network alignment algorithms can be categorized into two groups: global and local network alignment. Global network alignment algorithms search for the best alignment of entire networks, whereas local network alignment algorithms produce the aligned pairs of small sub-networks with the highest scores. In this survey, we summarize prominent network alignment algorithms in both categories. We also present the methods to evaluate network alignment algorithms. When we compare the evaluation results of selected network alignment algorithms, PrimAlign outperformed the other global network alignment algorithms. Among local network alignment algorithms, LeP-rimAlign was superior to the competitors. We conclude with a future direction to expand the applicability of network alignment techniques.