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

Oleksii Kuchaiev and Nataša Pržulj

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

Downloads

Download MI-GRAAL
Supplementary information: Supplementary Figure 1 and Supplementary Files 1–3, as one zip file

How to run MI-GRAAL

MI-GRAAL has been tested on Gentoo and Mandriva Linux, but should work on other distributions.
Download and unpack MI-GRAAL using the link above.
MI-GRAAL accepts networks in LEDA .gw format.
You need Python installed.
Run ./MI-GRAALRunner.py without parameters to see usage directions.
The number of nodes in the first network must not be greater than the number of nodes in the second network.

Example

In the folder where you unpacked MI-GRAAL:

./MI-GRAALRunner.py testGraph1.gw testGraph2.gw result -p 3

Converting an edge list to `.gw`

If your network is an edge list:

node1 node2
node3 node4
...

convert it with the list2leda script included in the MI-GRAAL download:

./list2leda edgelist.txt >> graph.gw

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

Other network alignment algorithms

Citation

O. Kuchaiev and N. Pržulj. Integrative network alignment reveals large regions of global network similarity in yeast and human. Bioinformatics 27(10), 1390–1396 (2011). https://doi.org/10.1093/bioinformatics/btr127