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Table 6 Algorithms used in this study and their key characteristics

From: Global multiple protein-protein interaction network alignment by combining pairwise network alignments

Algorithm

Commandline arguments

Node alignment

Notes

IsoRankN

--K 30 --thresh 1e-4 --alpha 0.9 --maxveclen 1000000

many-to-many

native MNA

NETAL

-a 0.0001 -b 0 -c 0.5 -i 2

one-to-one

no BLAST

PINALOG

none

primarily one-to-one

 

SMETANA

none

many-to-many

native MNA

  1. PINALOG and SMETANA do not require specific arguments when running the respective commandline implementations. Arguments for IsoRankN and NETAL have been used following recommendations by the authors in the literature and can be used to specify parameters that control the internal cost functions and put limits on iterations and other data that influence running time and memory requirements.