This package implements AligNet, a novel alignment algorithm aimed to obtain a global pairwise alignment of protein interaction networks, but also, to analyze the networks from the topological study of their modularization. AligNet obtains biological meaningful modules of a PPI network considering an overlapping clustering based on a similarity score between pairs of proteins, which is defined considering both their topological and their biological information. The analysis of the networks consists of the study of some topological features of the modules. Then, AligNet is able to obtained a well defined global pairwise alignment from the local alignment of the modules, which improved the results of the previous algorithms in the tests that we performed. The novelty of our tool AligNet is that on one hand, it is a tool for the global pairwise alignment of protein interaction networks and, on the other hand, it is also a tool for the analysis of a protein interaction network. The main advantage of AligNet, is that the analysis of the networks to be aligned is performed before the alignment itself. This entails that before computing the alignment we know wether the networks are well studied or, on the contrary, we can infer that they are not. Since the goodness of the alignment is related to the goodness of the networks, knowing in advance the networks accuracy is important to understand the final alignment.
|Author||Adria Alcala [aut, cre], Ricardo Alberich [aut], Merce Llabres [aut], Francesc Rossello [aut], Gabriel Valiente [aut]|
|Maintainer||Adria Alcala <[email protected]>|
|Package repository||View on GitHub|
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