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The local alignment is an important aspect of the analysis of protein-protein interaction networks that may lead to the identification of evolutionary related complexes.

AlignNemo is a novel algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that related in sequence and topology. The subnetworks have a general topology and need not to correspond to specific interaction patterns thus more closely fit the models of functional complexes proposed in the literature.

The algorithm is able to handle sparse interaction data with an expansion process that includes densely connected as well as sparsely connected subgraphs.

Here you can find more details about AlignNemo.

AlignNemo is currently implemented in Java and it is freely available for academic purposes.

Download AlignNemo, Installation Manual and Test Datasets: