Algorithms for detecting protein complexes in PPI networks: an evaluation study

Since protein complexes play important biological roles in cells, many computational methods have been proposed to detect protein complexes from protein-protein interaction (PPI) data. In this paper, we first review four reputed protein-complex detection algorithms (MCODE[2], MCL[21], CPA[1] and DECAFF[14]) and then present a comprehensive evaluation among them on two popular yeast PPI data3. We also discuss their relative strengthes and disadvantages to guide interested researchers.PRIB 2008 proceedings found at: http://dx.doi.org/10.1007/978-3-540-88436-