Figure 3

Benchmarks. CPU time and memory requirements of Proteinortho. (a) The speed benchmark was performed using an E. coli strain with 4132 proteins on an eight core Intel Xeon system using one thread (1) and eight threads (8) at 2.33 GHz. The encoded proteins were used multiple times to simulate multiple (identical) species. This is the worst case scenario for Proteinortho since in this case every protein has a link to at least one protein in every other species. Proteinortho is significantly faster than OrthoMCL. Using multiple threads we observe a substantial speed up. (b) The memory benchmark is performed using the same set as in (a). OrthoMCL quickly exhausts memory for larger sets. Proteinortho clearly performs more efficient, even though this artificial scenario is a more complex case than real world analysis. Both benchmarks outline that Proteinortho allows comprehensive studies which were not possible before.