NetworkBLAST protocols

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NetworkBLAST specifications

Information


Unique identifier OMICS_04885
Name NetworkBLAST
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for NetworkBLAST

NetworkBLAST in pipeline

2007
PMCID: 1847944
PMID: 17353930
DOI: 10.1038/msb4100129

[…] nodes of c. starting from single nodes, clusters are gradually grown as long as the cluster property of the added nodes and the density of the cluster both exceed a certain threshold., proposed the networkblast algorithm for detecting protein modules in protein interaction networks. each candidate set of proteins is assigned a likelihood ratio score that measures its fit to a protein complex […]


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NetworkBLAST in publications

 (18)
PMCID: 4926396
PMID: 27258269
DOI: 10.3390/ijms17060862

[…] measured by a “similarity score”. the core of the graph similarity search is the similarity scores that each method proposes. three commonly-used subgraph theoretical algorithms are graphgrep [], networkblast [] and saga []. graphgrep is a hash indexing-based method for subgraph matching, which allows efficient filtering by selecting the most relevant subgraphs from the relevant graphs. […]

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

[…] network. the comparisons made by previous studies show that alignnemo, alignmcl [] and damalign succeed in detecting more conserved complexes than previous methods [, ], 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 […]

PMCID: 5270500
PMID: 28194172
DOI: 10.1186/s13637-015-0022-9

[…] degree of protein sequence similarity and the interaction quality. in the process, gaps and mismatches are allowed to account for evolution variations and experimental errors in pathway structure., networkblast [] is an extension of pathblast that aims to identify not just simple linear pathways (as pathblast does) but also more complex network structures, e.g., dense functional modules […]

PMCID: 4313693
PMID: 25699028
DOI: 10.3389/fmicb.2015.00036

[…] these predicted ppis form the “bootstrap” ppis and will be used in a graph-based transfer approach. in this graph-based transfer method, we first align the ppi graphs of the two host organisms using networkblast (sharan et al., ). the human ppi network was obtained from the hprd database (prasad et al., ) and the plant-plant ppis from tair database (lamesch et al., ). the algorithm aligns […]

PMCID: 3996886
PMID: 24800226
DOI: 10.1155/2014/439476

[…] [], where each larger network is decomposed into a collection of smaller subnetworks in order to compute the alignment of the two networks as the optimal alignment of the subnetworks., a series of networkblast algorithms have been reported for the global alignment of networks. for example, pathblast [] is the first one of such algorithms to search for high-probability pathway alignments […]


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NetworkBLAST institution(s)
School of Computer Science, Tel Aviv University, Tel Aviv, Israel

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