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NetAligner specifications

Information


Unique identifier OMICS_07523
Name NetAligner
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Publications for NetAligner

NetAligner citations

 (4)
library_books

GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks

2015
Sci Rep
PMCID: 4499810
PMID: 26165520
DOI: 10.1038/srep12074

[…] ed on an explicit evolutionary model, and then the alignment is extended outwards from the seed along network edges, incorporating as many other protein pairs as possible and optimizing on the score. NetAligner, for example, assumes that interacting proteins evolve at similar rates as part of scoring edge mismatches and gaps. MaWISH formulates an evolutionary model consisting of three events: matc […]

library_books

Detecting conserved protein complexes using a dividing and matching algorithm and unequally lenient criteria for network comparison

2015
PMCID: 4487215
PMID: 26136815
DOI: 10.1186/s13015-015-0053-5

[…] ], such as Mawish, NetworkBlast,PHUNKEE and Produles. The reason may be considering indirectly connected node pairs in one network is robust against missing interactions in original network. Although NetAligner employs more lax criteria to introduce conserved interactions, it also yields a lot of false positive conserved interactions, which reduces its performance of detecting conserved complexes. […]

library_books

The post genomic era of biological network alignment

2015
EURASIP J Bioinform Syst Biol
PMCID: 5270500
PMID: 28194172
DOI: 10.1186/s13637-015-0022-9

[…] lem. Intuitively, it greedily grows a subgraph starting from a seed with maximum gain with respect to the cost function; a bad move (negative gain) is allowed in order to bypass a poor local optimum. NetAligner [] is a pairwise aligner featuring pathway-to-interactome, complex-to-interactome, and interactome-to-interactome alignments. Also, it is able to perform both inter- and intra-species align […]

library_books

Increasing the precision of orthology based complex prediction through network alignment

2014
PeerJ
PMCID: 4045337
PMID: 24918034
DOI: 10.7717/peerj.413

[…] We performed all complex to interactome alignments using the NetAligner algorithm that we recently developed () and which is also available as a web server (). For all species combinations, we computed vertex and interaction conservation probabilities required […]

Citations

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NetAligner institution(s)
Institute for Research in Biomedicine (IRB) Barcelona, Department of Structural and Computational Biology, Joint IRB-BSC Program in Computational Biology, Barcelona, Spain

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