GRAAL (GRAph ALigner) Algorithm
Supplementary Information for: "Topological network alignment uncovers biological function and phylogeny"
Oleksii Kuchaiev*, Tijana Milenkovic*, Vesna Memisevic, Wayne Hayes, Natasa Przulj
* These authors contributed equally to this work
Corresponding author: Prof. Natasa Przulj, e-mail: natasa [AT] cs.ucl.ac.uk
How to run GRAAL:
- GRAAL has been tested on Gentoo and Mandriva Linux distributions. However, it should work with other distributions.
- Download and unpack the GRAAL using the link above.
- GRAAL accepts networks in LEDA .gw format.
- Your should have Python installed on your system
- Run "./GRAALRunner.py" without any parameters and it will display usage directions
- Number of nodes in the first network must not be greater than number of nodes in the second network
- Go to the directory where you unpacked GRAAL.
- In terminal type "./GRAALRunner.py 0.8 testGraph1.gw testGraph2.gw result"
How to convert network from edge list format to .gw file accepted by GRAAL:
If your network is in edge list format:
You can use "list2leda" script (part of CodeAndTestData.zip) to convert it into the format accepted by GRAAL.
Use it like this: "./list2leda edgelist.txt >> graph.gw"
Note that self-loops, directionality and double edges will be ignored.