Table 1

Main features of the graph clustering approaches presented in this study.

Restricted Neighborhood Search Clustering (RNSC)

Markov Clustering (MCL)

Molecular Complex Detection (MCODE)

Super-paramagnetic clustering (SPC)


Type

Local search cost based

Flow simulation

Local neighbourhood density search

Hierarchical

Allow multiple assignations

No

No

Yes

No

Allow unassigned nodes

No

No

Yes

No

Edge-weighted graphs supported

No

Yes

No

Yes

First application

Protein complex prediction

Protein family detection

Protein complex detection

Other applications

/

Identification of ortholog groups, protein complexes, peer-to-peer node clustering, image retrieval, Word Sense Discrimination, molecular pathway discovery, structural domains, ...

/

Image clustering, microarray data clustering, protein complexes detection, protein structure classification, identification of ortholog groups, ...

Availability

Upon request

http://micans.org/mcl/ webcite

ftp://ftp.blueprint.org/pub/BIND/README webcite

Upon request

Developper

King AD

Van Dongen S

Bader GD and Hogue CWV

Blatt M, Wiseman S, Domany E

References

[21]

[35]

[19]

[18]


Brohée and van Helden BMC Bioinformatics 2006 7:488   doi:10.1186/1471-2105-7-488

Open Data