Motivation: Graph drawing algorithms are often used for visualizing relational information, but a naive implementation of a graph drawing algorithm encounters real difficulties when drawing large-scale graphs such as protein interaction networks. Results: We have developed a new, extremely fast layout algorithm for visualizing large-scale protein interaction networks in the three-dimensional space. The algorithm (1) first finds a layout of connected components of an entire network, (2) finds a global layout of nodes with respect to pivot nodes within a connected component and (3) refines the local layout of each connected component by first relocating midnodes with respect to their cutvertices and direct neighbors of the cutvertices and then by relocating all nodes with respect to their neighbors within distance 2. Advantages of this algorithm over classical graph drawing methods include: (1) it is an order of magnitude faster, (2) it can directly visualize data from protein interaction databases and (3) it provides several abstraction and comparison operations for effectively analyzing large-scale protein interaction networks.
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