Recent Advances in Molecular Technologies and Their Application in Pathogen Detection in Foods with Particular Reference to Yersinia

Table 1

Current software applications for microarray data analysis.

Software	Application	Provider	Platform	Web link
Array Designer	Primer design for microarray construction	Premier Biosoft International	Windows; Linux	http://www.premierbiosoft.com/dnamicroarray/index.html
ArrayMiner	Analysis tool for microarray gene expression data	Optimal Design	Mac OS; Windows	http://www.optimaldesign.com/ArrayMiner/ArrayMiner.htm
ArrayTrack	Database solution for managing, analyzing, and interpreting microarray gene expression data	National Center for Toxicological Research; U.S. Food and Drug Administration	Web-based
				http://www.fda.gov/ScienceResearch/BioinformaticsTools/
				Arraytrack/default.htm
				ArrayVision	Automated analysis of macro- and microarrays	GE Healthcare	Windows	http://www.gelifesciences.com/aptrix/upp01077.nsf/Content/
								Products?OpenDocument&ParentId=957136
				BAMarray	Detecting differentially expressed genes from microarray data using Bayesian analysis	Case Western Reserve University	Mac OS; Windows; Linux	http://www.bamarray.com/default.htm
BASE	Database solution for the massive amounts of data generated by microarray analysis	Lund University	Web-based	http://base.thep.lu.se/
Cluster	Perform a variety of types of cluster analysis and other types of processing on large microarray datasets	University of Tokyo	Mac OS; Windows; Linux/Unix	http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm
GenePattern	Gene expression analysis tools	Broad Institute, MIT	Web-based	http://www.broadinstitute.org/cancer/software/genepattern/desc/
				expression.html
GeneSifter	Tools for exploring the statistically significant interplay of the data with factors of biological relevance to understand the expression pattern in microarray data.	Geospiza Inc.	Web-based	http://www.geospiza.com/Products/AnalysisEdition.shtml
GenMAPP	Tools for visualizing data from gene expression experiments in the context of biological pathways.	Gladstone Institute, University of California at San Francisco	Windows	http://genmapp.org/
GenMaths XT	Analysis of high density microarrays and gene chips	Applied Maths	Windows	http://www.applied-maths.com/genemaths/genemaths.htm
Genowiz	A comprehensive multi platform software for microarray data analysis	Ocimum Biosolutions	Mac OS; Windows; Linux/Unix
				http://www3.ocimumbio.com/data-analysis-insights/
				analytical-tools/genowiz/
				Microarray tools	Including: a Comparative Genomic Hybridization (CGH) and expression microarray data analysis, data management and export system	J. Craig Venter Institute	Windows; Linux/Unix	http://www.jcvi.org/cms/research/software/#c622/
Partek Genomics Suite	Statistical analysis and data mining tools to facilitate powerful and intuitive exploratory data analysis	Partek Incorporated	Windows; Linux/Unix	http://www.partek.com/partekgs/
TreeArrange and Treeps	Software for displaying and manipulating hierarchical clustered data	University of Waterloo	Windows; Linux/Unix	http://monod.uwaterloo.ca/downloads/treearrange/
waviCGH	For the analysis and visualization of array-CGH data	Spanish National Cancer Center, Bioinformatics Unit	Web-based	http://wavi.bioinfo.cnio.es/