While topology-driven local network alignment has a wide variety of potential applications outside bioinformatics, here we focus on the alignment of Protein-Protein Interaction (PPI) networks.
We argue that this failure of topology alone is due to the sparsity and incompleteness of the PPI network data of almost all species, which provides the network topology with a small signal-to-noise ratio that is effectively swamped when sequence information is added to the mix.
The function of a protein is defined by its interaction partners.
Network alignment aims to uncover topologically similar regions in the protein-protein interaction (PPI) networks of two or more species under the assumption that topologically similar regions tend to perform similar functions.
SANA is one of many algorithms proposed for the arena of biological network alignment.