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mfinder specifications

Information


Unique identifier OMICS_05012
Name mfinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for mfinder

mfinder citations

 (48)
library_books

The origin of motif families in food webs

2017
Sci Rep
PMCID: 5700930
PMID: 29170384
DOI: 10.1038/s41598-017-15496-1

[…] lgorithm,. This preserves both the total number of nodes (species) and the links (trophic interactions) in the network. The generation of randomized networks and counts of triads was carried out with mfinder, the algorithm used by Milo et al. in their seminal work on network motifs,.It is important to emphasize that the TSP is a relative measure of which triads are over- and under-represented with […]

call_split

NemoProfile as an efficient approach to network motif analysis with instance collection

2017
BMC Bioinformatics
PMCID: 5657038
PMID: 29072139
DOI: 10.1186/s12859-017-1822-6
call_split See protocol

[…] h the size of motifs, therefore even listing them is intractable. As an example, there are 11,716,571 patterns for motif size 10, as shown in Table  Many motif search programs are also available []: MFinder [], FANMOD [], Kavosh [], Mavisto [], and NeMoFinder [] follow the network-centric methods. Motif-centric methods are available with Grochow’s [], and MODA []. However, most of them provide on […]

library_books

A data driven modeling approach to identify disease specific multi organ networks driving physiological dysregulation

2017
PLoS Comput Biol
PMCID: 5521738
PMID: 28732007
DOI: 10.1371/journal.pcbi.1005627

[…] We completed a number of analyses in which we utilized publicly available data and software tools, as described in detail below.Network motif analysis: We used the mfinder tool to search for specific network motifs associated with cellular adaptation [, ]. We visualized the detected subnetworks using Cytoscape [].Genetic analysis: The genomes of numerous rat str […]

library_books

Network Analysis Reveals A Signaling Regulatory Loop in the PIK3CA mutated Breast Cancer Predicting Survival Outcome

2017
PMCID: 5414713
PMID: 28392480
DOI: 10.1016/j.gpb.2017.02.002

[…] d a scaling factor of 100,000 to the heating scores and then conducted data transformation using the median centering and z-score between sample approach . The network motifs were extracted using the mFinder tool. The detailed description of using the tool has been described previously .PAM50 proliferation score was measured based on differential expression of the 11 proliferation genes, including […]

library_books

Inferring Microbial Interactions in the Gut of the Hong Kong Whipping Frog (Polypedates megacephalus) and a Validation Using Probiotics

2017
Front Microbiol
PMCID: 5371668
PMID: 28424669
DOI: 10.3389/fmicb.2017.00525

[…] at the genus level, MetaMIS can systematically examine interaction patterns, such as mutualism or competition; only the top 25% of interacting relationships were considered in this study. We used the mfinder tool (Milo et al., ) to identify significant 3-node directed motifs that contain two directed edges pointing to the same node. This process was repeated 100 times and all relationships that pa […]

call_split

Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients

2016
PMCID: 5093780
PMID: 27746285
DOI: 10.1016/j.gpb.2016.02.005
call_split See protocol

[…] ee, and average stress centralization are all topological properties of a node group and can be used in this kind of test.We analyzed the local structures of a network by finding network motifs using mfinder1.2 . For non-directed networks, we used mfinder1.2 to find the numbers of all the 6 tetrads present in the real network and in 100 random networks created by switching edges. For each kind of […]

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mfinder institution(s)
Department of Molecular Cell biology, Weizmann Institute of Science, Rehovot, Israel

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