GMOseek: a user friendly tool for optimized GMO testing

BMC Bioinformatics

Table 2 Comparison of GMOtrack and GMOseek screening strategies

Dataset name	Expected cost (event-specific assays only)	Lowest analytical cost GMOtrack	Combination GMOtrack (number assays)	Coverage GMOtrack (%)	Lowest analytical cost GMOseek	Combination GMOseek (number assays)	Coverage GMOseek (%)
GMO_EU_2005.tab	515.42	234.24	4	100	234.24	4	100
GMO_EU_2008.tab	557.78	376.73**	3	86	301.21	6	100
GMO_EU_2010.tab	1256.72	561.72**	3	96	429.06*	9*	100*
GMO_EU_2012.tab	1701.5	861.49**	3	91	592.84*	12*	99*
GMO_all_2012.tab	5280.92	No solution	No solution	No solution	1907.30*	14*	82*

*Interrupted before optimal result found.
**GMOtrack constrains parameters set to m = 3 (number of screening assays in solution) and coverage = 80% (the minimal coverage (in percentage of the total GM events in the dataset) of screening assay combinations).
Expected cost (event-specific assays only): cost (in arbitrary unit) of a sample analysis if no screening strategy is followed and only event-specific assays are use.
Lowest analytical cost GMOtrack: cost (in arbitrary unit) of a sample analysis using the best screening assay combination proposed by GMOtrack.
Combination GMOtrack (number assays): number of screening assays to be performed when following the best screening assay combination proposed by GMOtrack.
Coverage GMOtrack (%): Coverage (in percentage of the total GM events in the dataset) of the best screening assay combination proposed by GMOtrack.
Lowest analytical cost GMOseek: cost (in arbitrary unit) of a sample analysis using the best screening assay combination proposed by GMOseek.
Combination GMOseek (number assays): number of screening assays to be performed when following the best screening assay combination proposed by GMOseek.
Coverage GMOseek (%): Coverage (in percentage of the total GM events in the dataset) of the best screening assay combination proposed by GMOseek.

ISSN: 1471-2105