Table 1

Processing benchmarks for GenTHREADER versus mGenTHREADER. The processing time required for the sequence-profile method GenTHREADER is compared to the profile-profile version of mGenTHREADER. The data was collected by running both methods on sequences from the Human proteome using 148 identical CPUs (1.3 GHz Pentium IIIs from the cs.ucl.ac.uk domain) over a period of 10 hours. The throughput was measured as the mean number of sequences with structural annotations per hour.

GenTHREADER

mGenTHREADER

Mean sequences per hour on 148 identical CPUs

1236

230

Mean sequences per hour on 1 CPU

8.35

1.55

Mean time for 1 Human sequence on 1 CPU (min)

7.18

38.61

Estimated time for all Human sequences on 1 CPU (days)

159.70

858.24

McGuffin et al. BMC Bioinformatics 2006 7:288   doi:10.1186/1471-2105-7-288