AligNet: alignment of protein-protein interaction networks
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RESEARCH
Open Access
AligNet: alignment of protein-protein interaction networks Adrià Alcalá1,2 , Ricardo Alberich1,2 , Mercè Llabrés1,2*
, Francesc Rosselló1,2 and Gabriel Valiente3
From 15th International Symposium on Bioinformatics Research and Applications (ISBRA’19) Barcelona, Spain. 3-6 June 2019 *Correspondence: [email protected] 1 Department of Mathematics and Computer Science, University of the Balearic Islands, E-07122 Palma de Mallorca, Spain 2 Balearic Islands Health Research Institute (IdISBa) E-07010 Palma de Mallorca, Spain Full list of author information is available at the end of the article
Abstract Background: All molecular functions and biological processes are carried out by groups of proteins that interact with each other. Metaproteomic data continuously generates new proteins whose molecular functions and relations must be discovered. A widely accepted structure to model functional relations between proteins are protein-protein interaction networks (PPIN), and their analysis and alignment has become a key ingredient in the study and prediction of protein-protein interactions, protein function, and evolutionary conserved assembly pathways of protein complexes. Several PPIN aligners have been proposed, but attaining the right balance between network topology and biological information is one of the most difficult and key points in the design of any PPIN alignment algorithm. Results: Motivated by the challenge of well-balanced and efficient algorithms, we have designed and implemented AligNet, a parameter-free pairwise PPIN alignment algorithm aimed at bridging the gap between topologically efficient and biologically meaningful matchings. A comparison of the results obtained with AligNet and with the best aligners shows that AligNet achieves indeed a good balance between topological and biological matching. Conclusion: In this paper we present AligNet, a new pairwise global PPIN aligner that produces biologically meaningful alignments, by achieving a good balance between structural matching and protein function conservation, and more efficient computations than state-of-the-art tools. Keywords: Protein-protein interaction network, Global alignment, Network matching, Functional consistency
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