Large-scale data analysis for robotic yeast one-hybrid platforms and multi-disciplinary studies using GateMultiplex

Table 1 The comparison of GateMultiplex to two most widely used software

	Language	GUI^a	Input file format	Adjustable parameters to identify positive events	Output files	Application
GateMultiplex	C++ (fastest)	Yes	Format-free	(1) Background noise cutoff (2) Reference cutoff (3) Bio/Tech replicates cutoff (4) Internal control cutoff (5) Positive cutoff	(1) Result file (2) Fold-change file (3) PNE file	(1) Yeast one-hybrid (2) Yeast two-hybrid (3) Drug development (4) Precision agriculture (5) Deep-sea fishery
SpotOn	Perl	NA	HDF plate format	(1) Reference cutoff^b	(1) Result file	(1) Yeast one-hybrid (2) Yeast two-hybrid
TIDY	Matlab	NA	HDF plate format	(1) Reference cutoff^c (2) Bio/Tech replicates cutoff^d	NA^e	(1) Yeast one-hybrid

^aThe users can operate the GUI without further installing additional programming language user interface
^bNamed as z score cutoff in the original paper. The negative control value could be adjusted, but the fold-change value is not adjustable
^cNamed as background threshold in the original paper with the function similar to reference cutoff in this article. The fold-change value could be adjusted, but the negative control value is not adjustable
^dNamed as uniformity coefficient in the original paper with the function similar to Bio/Tech replicates cutoff. Only technical replicates can be processed but not biological replicates
^eThe output results only showed on the command lines

ISSN: 1741-7007