MI-GRAAL (Matching-based Integrative GRAph ALigner) Algorithm

Oleksii Kuchaiev and Natasa Przulj

Corresponding author: Prof. Natasa Przulj, e-mail: natasa [AT] cs.ucl.ac.uk

How to run MI-GRAAL:

  • MI-GRAAL has been tested on Gentoo and Mandriva Linux distributions.
    However, it should work with other distributions too.
  • Download and unpack the MI-GRAAL using the link above.
  • MI-GRAAL accepts networks in LEDA .gw format.
  • Your should have Python installed on your system
  • Run "./MI-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

Sample Usage:

  • Go to the directory where you unpacked MI-GRAAL.
  • In terminal type "./MI-GRAALRunner.py testGraph1.gw testGraph2.gw result -p 3"

How to convert network from edge list format to .gw file accepted by MI-GRAAL:

If your network is in edge list format:

node1 node2
node3 node4

You can use "list2leda" script (part of CodeAndTestData.zip) to convert it into the format accepted by MI-GRAAL.
Use it like this: "./list2leda edgelist.txt >> graph.gw"
Note that self-loops, directionality and double edges will be ignored.

Other network alignment algorithms: