FANMOD specifications

Information


Unique identifier OMICS_05013
Name FANMOD
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Medium
Stability Stable
Maintained Yes

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Publication for FANMOD

FANMOD in publications

 (47)
PMCID: 5793192
PMID: 29337910
DOI: 10.3390/genes9010041

[…] than the un-interacted proteins, both of the biological motifs and modules play an important role in understanding complex biological processes. the identification of motifs was carried out with the fanmod tool [], with the conventional parameters (p value < 0.05, z score > 2, etc.). the functional modules were extracted using the netcarto program, which maximized the network modularity m […]

PMCID: 5679526
PMID: 29121052
DOI: 10.1371/journal.pone.0187426

[…] network biology at each time point. therefore, the mt, mm, and mtm class loops at 24h and 7d were searched for statistically significant functional network motifs via the motif detection tools fanmod []. while the computational problem of finding three and four node motifs is tractable, exhaustive enumeration becomes problematic for larger values of nodes, making such analysis impossible […]

PMCID: 5657038
PMID: 29072139
DOI: 10.1186/s12859-017-1822-6

[…] therefore even listing them is intractable. as an example, there are 11,716,571 patterns for motif size 10, as shown in table  table 1 , 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 […]

PMCID: 5388290
PMID: 28338825
DOI: 10.1093/gbe/evx036

[…] acid (k) varies between 1 and 12. we collate the entire network into isomorphic patterns (subgraphs), where one amino acid contacts ≥1 nucleotides, but internucleotide contacts are disregarded. fanmod standalone tool () is used to identify these subgraphs. the number of occurrences of each subgraph is enumerated in the input network. for example, we find 35 subgraphs with k = 7 (). next, […]

PMCID: 5215746
PMID: 27984591
DOI: 10.1371/journal.pcbi.1005283

[…] method []. hive plots were generated using the custom hiveplotter function written in python (python software foundation. python language reference, v3.5). 3-node network motifs were computed using fanmod []. additional network visualisations were created using cytoscape [] and dia (https://wiki.gnome.org/apps/dia/)., we thank oliver hobert, niels ringstad, and the caenorhabditis genetics […]


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FANMOD institution(s)
Institut für Informatik, Friedrich-Schiller-Universität Jena Ernst-Abbe- Jena, Germany

FANMOD reviews

 (2)
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li yan

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Desktop
I have not used the software yet, but I have found that the software has very little knowledge, it is difficult to find relevant information, I hope to buy books related to the software on some websites.
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Anonymous user #951

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I think the standalone tool (and hence the code associated with that) has a lot of limitations when used with a network of 20 or 30 million nodes. The tool easily crashes and even for subgraphs of size 6 or 7, it is not able to handle even 50000 nodes and a dense network.