Aligning Biological Networks with L-GRAAL (Lagrangian GRAphlet-based Network Aligner)
Noël Malod-Dognin and Nataša Pržulj
Corresponding author: Dr. N. Malod-Dognin, noel.malod@mbzuai.ac.ae
L-GRAAL is a global network alignment tool that combines an efficient solver based on Lagrangian relaxation with a scoring function based on the statistics of small induced subgraphs called graphlets.
Downloads
- L-GRAAL for Linux x64
- Supplementary material (PDF)
- Predicted interactions between yeast and human (XLS)
- PPI dataset: networks, graphlet degree signatures, and sequences
How to run L-GRAAL
To align two PPI networks, you need 5 input files:
- the two network files, in LEDA format (
.gw, see format description) - two files with the graphlet degree signatures of the networks’ nodes (the
.ndump2files produced by the providedncount4software) - a file with the sequence alignment scores (1 − e-values, −log(e-values), or bitscores) between the proteins of the two networks
Example, aligning R. norvegicus and S. pombe:
./L-GRAAL -Q RNorvegicus.gw -T SPombe.gw -q RNorvegicus.ndump2 -t SPombe.ndump2 -B blast_evalues.txt -o my_output
Run ./L-GRAAL.exe -h for the full list of parameters.
Other network alignment algorithms
Citation
N. Malod-Dognin and N. Pržulj. L-GRAAL: Lagrangian graphlet-based network aligner. Bioinformatics 31(13), 2182–2189 (2015). https://doi.org/10.1093/bioinformatics/btv130