Skip to main content

Table 2 Execution time in seconds for the comparison of the sequences listed in Table 1 under “pairwise comparison” (lowest execution time and memory consumption of each row are highlighted in bold). The comparison of mammalian chromosomes was also included to test the ability of GECKO and reference software packages to function when analysing very large datasets. The dictionary calculation time is included in the reported times, since the dictionary were not pre-calculated. “n.a.” indicates that resource problems prevented analysis execution and the presence of (*1) after some execution times indicates that the time was measured in a bigger machine because in such cases they were using more than 8GB of memory (more details of these cases in the Additional file 1 Section 3.3)

From: Breaking the computational barriers of pairwise genome comparison

  Gepard MUMmer Mauve
Comparison Time Memory Time Memory Time Memory
TYLCV-TYLCV-lr2 0.84 52824 0.00 2944 0.06 2800
BuchneraAPS-BuchneraBp 2.56 74808 0.44 11100 6.73 14304
E.colik12-E.coliO157 33.12 378412 10.63 79212 45.92 99880
D.Melanogaster-D.Pseudoobscura 238.34 716244 45.99 355272 294.92 379912
H.Sapiens-Chr1-P.Troglodytes-chr1 7 0 8 4 . 0 0 1 49788208 23226.001 15747168 >604800.00 n.a.
  LASTZ LAST GECKO
Comparison Time Memory Time Memory Time Memory
TYLCV-TYLCV-lr2 0.04 67388 0.00 3024 0.36 1564816
BuchneraAPS-BuchneraBp 0.46 71244 46.20 475912 1.60 1564816
E.colik12-E.coliO157 1.83 95884 109.00 1972028 17.20 1564816
D.Melanogaster-D.Pseudoobscura 19.64 190448 1593.00 5436716 48.72 1564816
H.Sapiens-Chr1-P.Troglodytes-chr1 78360.00 5782352 n.a. 312065840 11848.15 1564816