Aligning Biological Networks with L-GRAAL (Lagrangian GRAphlet-based network Aligner)
Noel Malod-Dognin and Natasa Przulj
Corresponding author: Dr. N. Malod-Dognin, e-mail: n.malod-dognin [AT] cs.ucl.ac.uk
L-GRAAL is a novel global network alignment tool, which combines an efficient solver based on Lagrangian relaxation with a scoring function based on the statistics of small induced subgraphs called graphlets.
Two files containing the graphlet degree signatures of the networks' nodes (the .ndump2 files produced by the provided ncount4 software)
A file containing the sequence alignment scores (1-evalues, or -log(evalues), or bitscores) between the proteins of the two networks
Example, when aligning RNorvegicus and SPombe:
``./L-GRAAL -Q RNorvegicus.gw -T SPombe.gw -q RNorvegicus.ndump2 -t SPombe.ndump2 -B blast_evalues.txt -o my_output''
You can alternatively run ``./L-GRAAL.exe -h'' to get the complete list of parameters.