2026-04-29T15:25:25Zhttps://repisalud.isciii.es/rest/oai/request

oai:repisalud.isciii.es:20.500.12105/228682024-11-29T03:42:10Zcom_20.500.12105_15322com_20.500.12105_2051col_20.500.12105_16967

00925njm 22002777a 4500 dc Alcala, Adria author Alberich, Ricardo author Llabres, Merce author Rossello, Francesc author Valiente, Gabriel author 2020-11-18 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. Alcala A, Alberich R, Llabres M, Rossello F, Valiente G. AligNet: alignment of protein-protein interaction networks. BMC Bioinformatics. 2020 Nov 18;21 Suppl 6:265. 10.1186/s12859-020-3502-1 1471-2105 BMC Bioinformatics http://hdl.handle.net/20.500.13003/15886 33203353 L633454222 2-s2.0-85096148502 https://hdl.handle.net/20.500.12105/22868 594994500007 Protein-protein interaction network Global alignment Network matching Functional consistency AligNet: alignment of protein-protein interaction networks