Shared probe design and existing microarray reanalysis using PICKY

BMC Bioinformatics

Table 2 PICKY execution time and result under two different design constraints.

Model species	Gene set size	More sensitive design	More relaxed design
*E. coli*	5317 genes 4 848 788 bp	2-CPU: 0 h 9 m 4651 probes	4-CPU: 0 h 7 m 4852 probes
Bee	11 324 genes 6 022 273 bp	2-CPU: 0 h 11 m 10 237 probes	4-CPU: 0 h 17 m 10 995 probes
Yeast	6702 genes 9 081 699 bp	2-CPU: 0 h 22 m 5892 probes	2-CPU: 0 h 35 m 6164 probes
*P. falciparum*	9518 genes 10 749 024 bp	2-CPU: 0 h 4 m 4199 probes	4-CPU: 0 h 55 m 7481 probes
Zebrafish	12 238 genes 23 015 888 bp	4-CPU: 0 h 22 m 9535 probes	2-CPU: 3 h 2 m 10 749 probes
*Drosophila*	18 962 genes 32 217 720 bp	2-CPU: 1 h 2 m 12 611 probes	4-CPU: 2 h19 m 15 686 probes
Chicken	26 236 genes 32 759 147 bp	4-CPU: 0 h 23 m 15 931 probes	2-CPU: 4 h 21 m 22 509 probes
*C. elegans*	30 935 genes 34 783 951 bp	2-CPU: 0 h 41 m 16 887 probes	4-CPU: 3 h 37 m 25 602 probes
*Arabidopsis*	28 952 genes 36 327 482 bp	2-CPU: 1 h 3 m 18 297 probes	2-CPU: 8 h 26 m 26 608 probes
Maize	58 579 genes 39 022 169 bp	2-CPU: 0 h 48 m 21 993 probes	2-CPU: 8 h 9 m 48 620 probes
Mouse	35 284 genes 68 639 601 bp	4-CPU: 0 h 23 m 11 450 probes	4-CPU: 9 h 36 m 28 435 probes
Human	28 205 genes 72 748 721 bp	4-CPU: 0 h 19 m 9134 probes	4-CPU: 8 h 58 m 25 080 probes
Rice	61 251 genes 94 194 626 bp	2-CPU: 10 h 1 m 39 094 probes	4-CPU: 10 h 33 m 43 376 probes

Two probe sets are designed for each of the 13 model species. Under "More sensitive design", fewer probes can be found but they need less time to compute. Under "More relaxed design", more probes can be found but they require additional thermodynamic comparisons. These probe sets were computed either on a 2-CPU Opteron 2.0 GHz workstation or on a 4-CPU Opteron 2.2 GHz server with slightly higher memory overhead; thus, the computation time spent are comparable between the two machines (e.g., 10 minutes on the 2-CPU workstation is roughly equal to 5 minutes on the 4-CPU server). The data from this table are also drawn in Figure 6.

ISSN: 1471-2105