Table 2

GraphAlignment and Græmlin performance on empirical bio-molecular networks
Comparison Escherichia coli vs. Caulobacter crescentus Escherichia coli vs. Campylobacter jejuni
Algorithm GraphAlignment Græmlin Blast BBH GraphAlignment Græmlin Blast BBH
NA 445 467 462 354 363 357
NC 319 309 (333) 333 247 241 (253) 253
NO 331 331 331 255 255 255
NC / NA [%] 71.7 66.2 (71.3) 72.1 69.8 66.3 (69.7) 70.9
NC / NO [%] 96.4 93.4 (101) 101 96.9 94.5 (99.2) 99.2
Edge / vertex score 2505 / 2774 - - 2592 / 2253 - -
Comparison Homo sapiens vs. Mus musculus Homo sapiens vs. Saccharomyces cerevisiae
Algorithm GraphAlignment Græmlin Blast BBH GraphAlignment Græmlin Blast BBH
NA 7919 7907 7862 2369 1213 988
NC 5743 6327 6375 581 869 (882) 808
NO 6402 6402 6402 965 965 965
NC / NA [%] 72.5 80.0 (80.0) 81.1 24.5 71.6 (72.7) 81.8
NC / NO [%] 89.7 98.8 (98.8) 99.6 60.2 90.1 (91.4) 83.7
Edge / vertex score 2034 / 64661 - - 20025 / 3963 - -

Protein-protein interaction networks. For Græmlin, the values are calculated using the strict rule. Values obtained following the relaxed rule are given in parentheses. For GraphAlignment, the relative contributions of the edge and node score are also given. Results obtained using BLAST bidirectional best hit are provided for comparison.

Kolář et al.

Kolář et al. BMC Systems Biology 2012 6:144   doi:10.1186/1752-0509-6-144

Open Data