Core & Peel

Core & Peel, is a web interface provides users with a tool to find dense subgraphs in a PPI network.
The Core & Peel, web interface allows you to:
  • run the Core & Peel, algorithm with several parameter settings on custom data or on example data;
  • download the outcome of the algorithm and the sample datasets.

Enter Core & Peel

How to use Core & Peel
You can upload an ASCII file containing the list of the edges of the graph or use one of the five data files provided as default:

Dataset Specie Reference proteins interactions
DIP yeast Xenarios et al. 2000 4,637 21,107
Biogrid yeast Stark et al. 2006 6,686 220,499
String yeast Franceschini et al. 2013 5,590 133,082
Biogrid homo sapiens Stark et al. 2006 18,170 137,775
String homo sapiens Franceschini et al. 2013 12,717 193,105


The parameters that can be set are:
  • Neighborhood radius (r=1, r=2), r=1 the default is recommended value.
  • Minimum density of the subgraphs sought. maximum's default is 100\%.
  • Subgraph minimum size (either as an absolute number >=3, or as a proportion to the average degree of the PPI network).
  • Filtering policy (from more aggressive (f=0) to looser (f=2).

The parameters chosen will influence the running time of the method.


[1] Xenarios, I., Rice, D.W., Salwinski, L., et al. (2000) DIP: the database of interacting proteins Nucleic Acids Res, 28, 289–291.
[2] Stark, C., Breitkreutz, B.J., Reguly, T., et al. (2006) BioGRID: a general repository for interaction datasets, Nucleic Acids Res, 34, D535–539.
[3] Franceschini A, Szklarczyk D, Frankild S, et al. (2013) STRING v9.1: protein-protein interaction networks, with increased coverage and integration, Nucleic Acids Res, 41, D808–D815.


Please, send any comments, bug reports, opinions to: BioAlgo Group
Styled and mantained by:
M. Elena Renda