C-GRAAL: Common-Neighbors-Based Global GRAph ALignment Algorithm

Supplementary material

Vesna Memišević and Nataša Pržulj

Corresponding author: Prof. N. Pržulj, natasa.przulj@mbzuai.ac.ae

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V. Memišević and N. Pržulj. C-GRAAL: Common-neighbors-based global GRAph ALignment of biological networks. Integrative Biology 4, 734–743 (2012). PMID: 22234340
Supplementary material (PDF)

Executables

Networks

Alignments

Best alignments

Predictions

How to run C-GRAAL

Download CGRAAL_unix64 from the link above. C-GRAAL accepts networks in LEDA .gw format.
Run ./CGRAAL_unix64 without parameters to see usage directions.

Usage:

./CGRAAL_unix64 net1.gw net2.gw similarity.file output1.file output2.file

net1.gw: first network (.gw format)
net2.gw: second network (.gw format)
similarity.file: similarity between nodes in net1 and net2, in the format nodeXNet1 nodeYNet2 similarity
output1.file: alignment output as node_Net1 node_Net2, with nodes as numbers
output2.file: alignment output as node_Net1 node_Net2, with nodes as names

The number of nodes in the first network must not be greater than the number of nodes in the second network.

If you get a “permission denied” error, run chmod +x CGRAAL_unix64 first.

Converting an edge list to `.gw`

If your network is an edge list:

node1 node2
node3 node4
...

convert it with the list2leda script:

./list2leda edgelist.txt >> graph.gw

Self-loops, edge directions and duplicate edges are ignored.

Figures

The largest common connected component of the best alignment for each pair:

Yeast - Human	C. jejuni - E. coli	M. loti - Synechocystis sp. PCC6803
F. tularensis - H. sapiens	B. anthracis - H. sapiens	Y. pestis - H. sapiens

Other network alignment algorithms

Notes

All p-values in the paper were calculated with MATLAB 2007. Newer MATLAB versions use a different output precision, so their p-values may differ from those obtained with the 2007 version (e.g. old version: 1.7E-9, newer version: 0.0).