title: Using MCL to extract clusters from networks.
abstract: MCL is a general purpose cluster algorithm for both weighted and unweighted networks. The algorithm utilises network topology as well as edge weights, is highly scalable and has been applied in a wide variety of bioinformatic methods. In this chapter, we give protocols and case studies for clustering of networks derived from, respectively, protein sequence similarities and gene expression profile correlations.
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK. svd@sanger.ac.uk
authors.forename: Stijn
authors.initials: S
authors.lastname: van Dongen
authors.forename: Cei
authors.initials: C
authors.lastname: Abreu-Goodger
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D055641:Mathematical Concepts; D017386:Sequence Homology, Amino Acid; D012984:Software