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MNAligner specifications


Unique identifier OMICS_24038
Name MNAligner
Alternative name Molecular Network Aligner
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB
Computer skills Advanced
Version 1.0
Stability Beta
Maintained Yes



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  • person_outline Luonan Chen <>
  • person_outline Xiang-Sun Zhang <>

Publication for Molecular Network Aligner

MNAligner in publications

PMCID: 5148114
PMID: 27936108
DOI: 10.1371/journal.pone.0168044

[…] matching scores in the similarity objective function. then, the alignment of pathways is solved by maximizing the similarity objective function between two pathways over all feasible combinations. mnaligner [] is one example of such methods. mnaligner uses the integer quadratic programming to formulate the alignment of two pathways and find conserved patterns between pathways. to align […]

PMCID: 3221619
PMID: 22024468
DOI: 10.1186/2043-9113-1-28

[…] high-throughput data (ntrninfer), inferring protein-protein interactions by parsimony principle (ninferppi), inferring protein-protein interactions based on multi-domain cooperation (nmdcinfer), molecular network aligner (nmnaligner), detecting drug targets in metabolic networks by integer linear programming (nmetailp), protein structure alignment tool based on multiple objective […]

PMCID: 2782142
PMID: 19997609
DOI: 10.1371/journal.pone.0008070

[…] the tutorial files in the pathblast plugin of software cytopscape (version 1.1, and they were used for the validation of a network alignment algorithm called mnaligner ., for aligning the synthetic networks, we parameterized the hmms as follows. we set the transition scores directly based on the “adjacent matrices” given in , which contain […]

PMCID: 2687956
PMID: 19477994
DOI: 10.1093/bioinformatics/btp202

[…] extract conserved complexes. mawish (koyutürk et al., ) merged pairwise interaction networks into a single alignment graph and treated network alignment as a maximum weight induced subgraph problem. mnaligner (li et al., ) described an integer quadratic programming (iqp) model to identify conserved substructures., recently, several network alignment algorithms have been developed that can align […]

MNAligner institution(s)
Beijing Wuzi University, Beijing, China; Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China; Graduate University of Chinese Academy of Sciences, Beijing, China; Institute of Systems Biology, Shanghai University, Shanghai, China; Osaka Sangyo University, Osaka, Japan; ERATO Aihara Complexity Modelling Project, JST, Tokyo, Japan; Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
MNAligner funding source(s)
Supported by Important Research Direction Project of CAS ‘Some Important Problems in Bioinformatics’, National Natural Science Foundation of China under Grant No.10631070, 60503004, the National Basic Research Program (973 Program) under Grant No. 2006CB503910, K.G.Wang Education Foundation Hong Kong and by JSPS-NSFC Collaboration Project.

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