Shared probe design and existing microarray reanalysis using PICKY

BMC Bioinformatics

Table 1 Comparison of design results using the linear and nonlinear salt effect equations at different salt concentrations.

Salt Conc.	Linear Probes	Nonlinear Probes	Same Probes	Overlap Probes	Average Temperature Difference	Medium Temperature Difference
50	3352	3254	1020	2380	2.70	2.38
100	3352	3281	1301	2501	1.15	0.62
200	3352	3310	1662	2630	1.80	1.37
300	3352	3321	1977	2809	1.80	1.55
400	3352	3326	1734	2307	2.53	1.67
500	3352	3332	2253	2780	1.75	1.35
600	3352	3339	2333	2754	1.62	1.12
700	3352	3340	2409	2698	1.46	0.86
800	3352	3342	2475	2668	1.25	0.58
900	3352	3342	2544	2633	1.01	0.29
950	3352	3344	2565	2617	0.89	0.14
1000	3352	3352	3352	3352	0.00	0.00

Salt concentrations are shown in milliMolar (mM). The "Linear Probes" are the same but the "Nonlinear Probes" vary greatly at each salt concentration. Comparing the two probe sets, the "Same Probes" and "Overlap Probes" columns show the number of their probes that are the same or overlapping. Although at each salt concentration the "Average" and "Medium" target melting temperatures of the two probe sets differ just slightly, the two probes sets do not converge until reaching the 1000 mM standard salt concentration level.

ISSN: 1471-2105