AlignNemo

[…] mappings. however, local aligners focus on the most conserved regions of the networks, and thus return very small alignments. although local aligners are not designed to align large networks (alignnemo, alignmcl and localali all encounter memory issues on our datasets), we were able to use alignnemo to align our smallest pair of networks, r. norvegicus ppi network (1,657 nodes and 2,330 […]

[…] of indirect connection between homologous proteins in the other network and connects two nodes in alignment graph if there is at least a pair of proteins in one network is directly connected. alignnemo [] adopts less restrict criterion and constructs edges in alignment graph if a least a pair of proteins in one ppi network is directly or indirectly connected. netaligner [] adds edges […]

[…] indirect interactions (i.e., three-node paths) in one or both input networks. finally, netaligner searches again for connected components in such extended alignment graph, which are its output., alignnemo [] is a recent pairwise local aligner capable of handling sparse network data. it first uses the concept of a weighted alignment graph, in which nodes represent pairs of orthologs […]

[…] able to yield robust and accurate results. we may need to appropriately integrate multiple information sources to repress the noise in existing ppi datasets by borrowing strengths from each other. alignnemo [] is one of such recent efforts, which detects network clusters on an alignment network of two given ppi networks. alignnemo takes into account not only the network topology from two ppi […]