• EST clustering and analysis
  
• Proteomics
  
• Transcriptomics : clustering and analysis
  
• Transcriptomics : visualization
  
• Transcriptomics : normalization
  
• Transcriptomics : preprocessing
  
• Transcriptomics : probe design
  

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EST clustering and analysis

	Name	Description	Link
	ADEL	Analysis of Distribution of ESTs in cDNA Libraries	ADEL online
	BLAST on Unigene	Identification of an EST as a member of a Unigene cluster greatly enhanced the corresponding gene characterization
	Ensembl for SIGENAE	Ensembl : Sigenae EST ContigBrowser (Bos taurus, Gallus gallus, Oncorhynchus mykiss, Sus scrofa, Oryctolagus cuniculus)	Sigenae EST ContigBrowser
	EPA	integrated system for EST collection Processing and semi-automatic Annotation	EPA online
	EST analysis suite	a bioinformatics suite to perform EST data analysis	more information
	Significance of digital gene expression profiles	statistical analysis of digital transcription profiles data	homepage
	SNP detection	This system permits the detection via two different strategies : SNP detection in EST databases, and SNP detection in sequences produced by direct DNA sequencing.	webpage
	TGI Clustering tools	fast clustering of large EST datasets	TGI Software Tools

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Proteomics

	Name	Description	Link
	ASCQ_ME	data mining program for the identification of proteins from mass spectrometry raw data	homepage
	BlastSets	New strategy for the representation and the integration of biomolecular knowledge at a cellular scale.	webpage
	Gelprint	generates an in silico 2D-gel from the theoretical pI (isoelectric point) and Mw (molecular weight) data for a set of proteins	Gelprint online
	Glycoproteomics	automatic interpretation of glycans and glycoproteins mass spectra	description in Lille
	Pepline	A tool for high throughput proteomics developped by the Helix team.	Pepline’s webpage
	Predotar	a neural-network-based prediction program capable of identifying ER signal peptides and mitochondrial or plastid transit peptides	Predotar online

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Transcriptomics : clustering and analysis

	Name	Description	Link
	AMIADA	an integrated computer program for organizing, exploring, visualizing, and analyzing microarray data	homepage
	AnovArray	SAS package relying on ANOVA (Analysis of Variance) and multiple hypothesis testing based on FDR (False Discovery Rate)
	AQBC	Adaptive quality-based clustering of gene expression profiles
	Array File Maker	generates input files for clustering, helps prepare colored figures and Venn diagrams, and can uncover aneuploidy in yeast microarray data.	homepage
	Autoclass	Unsupervised classification software.
	BLAST on Unigene	Identification of an EST as a member of a Unigene cluster greatly enhanced the corresponding gene characterization
	BRB Array tool	an integrated package for the visualization and statistical analysis of DNA microarray gene expression data using an Excel front end	homepage
	Cleaver	facilities for visualization, classification, and clustering	homepage
	Clusfavor	Cluster and Factor Analysis Using Varimax Orthogonal Rotation
	ClusPackX	Differential expression test, classification and visualisation of expression class profiles.
	Cluster	A short program for PCA and Hierarchical clustering
	Cluster analysis	Online software for unsupervised clustering	online form
	ClusterW	Clustering with clustalW
	D-chip	a software package implementing model-based expression analysis of oligonucleotide arrays and several high-level analysis procedures	homepage
	Data processing of time course data	A suite of Excel spreadsheet templates	homepage
	Difftool	Building and visualizing protein clusters
	DNA Microarray Data Analysis Script
	EPCLUST	EBI’s clutering program
	Expression Profiler	cluster analysis, pattern discovery, pattern visualization, study and search Gene Ontology categories, ...	homepage
	fcluster	a tool for fuzzy cluster analysis	homepage
	GeneCluster	filter and preprocess data in a variety of ways, cluster expression profiles using the SOM algorithm, view the results.	webpage
	Genesight	explore large data sets from multiple experimental groups using advanced normalization, visualization, and statistical decision support tools	webpage
	GeneViz	Double Conjugated Clustering	software list
	GEPAS	Gene Expression Pattern Analysis Suite	homepage
	Identitag	Tag-to-gene mapping for SAGE data
	J-express	multidimensional scaling, clustering, and visualisation	homepage
	MAANOVA	a set of functions written in Matlab for the analysis of variance on microarray data	webpage
	MADTools	composed of a local data base (MADSTAR), data processing software (MADSCAN), comprehension support tool (MADSENSE) and an automatic analysis of sequences software
	MAExplorer	MicroArray Explorer
	MeV	Multi experiment Viewer
	Normalise suite	normalise individual arrays across the entire array or by subgrids, group individual arrays into a project and take specific projects and generate results plots	homepage
	SAM-software	Supervised learning software for genomic expression data mining	homepage
	SMA	R-package : Statistics for Microarray Analysis	homepage
	Snob	uses the Minimum Message Length principle to do clustering	Snob page
	SOTA	Self Organising Tree Algorithm	online form
	svmlight	an implementation of Support Vector Machines which solves classification and regression problems	homepage
	Treeview	Graphically browse results of clustering and other analyses from Cluster	Eisen software
	Xcluster	A fast and efficient software for clustering	Xcluster homepage

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Transcriptomics : visualization

	Name	Description	Link
	AGScan	a micro-array image processing software	AGScan’s webpage
	Array File Maker	generates input files for clustering, helps prepare colored figures and Venn diagrams, and can uncover aneuploidy in yeast microarray data.	homepage
	ArrayPlot	Normalization software, with some visualization tools	homepage
	BRB Array tool	an integrated package for the visualization and statistical analysis of DNA microarray gene expression data using an Excel front end	homepage
	Clusfavor	Cluster and Factor Analysis Using Varimax Orthogonal Rotation
	ClusPackX	Differential expression test, classification and visualisation of expression class profiles.
	D-chip	a software package implementing model-based expression analysis of oligonucleotide arrays and several high-level analysis procedures	homepage
	Expression Profiler	cluster analysis, pattern discovery, pattern visualization, study and search Gene Ontology categories, ...	homepage
	Freeview	viewing and optimizing gene expression dendrograms	homepage
	Genesight	explore large data sets from multiple experimental groups using advanced normalization, visualization, and statistical decision support tools	webpage
	GEPAS	Gene Expression Pattern Analysis Suite	homepage
	J-express	multidimensional scaling, clustering, and visualisation	homepage
	MAExplorer	MicroArray Explorer
	Slcview	create image files from .cdt and .gtr files en masse from a Unix command prompt	homepage
	SOMview	Make Xcluster graphics	webpage
	SOTA	Self Organising Tree Algorithm	online form
	TreeMapClusterView	explore microarray data using a tree view	webpage
	Treeview	Graphically browse results of clustering and other analyses from Cluster	Eisen software

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Transcriptomics : normalization

	Name	Description	Link
	AMIADA	an integrated computer program for organizing, exploring, visualizing, and analyzing microarray data	homepage
	ArrayPlot	Normalization software, with some visualization tools	homepage
	BRB Array tool	an integrated package for the visualization and statistical analysis of DNA microarray gene expression data using an Excel front end	homepage
	D-chip	a software package implementing model-based expression analysis of oligonucleotide arrays and several high-level analysis procedures	homepage
	DNA Microarray Data Analysis Script
	Genesight	explore large data sets from multiple experimental groups using advanced normalization, visualization, and statistical decision support tools	webpage
	GEPAS	Gene Expression Pattern Analysis Suite	homepage
	MAANOVA	a set of functions written in Matlab for the analysis of variance on microarray data	webpage
	MAExplorer	MicroArray Explorer
	MarC-V	Microarray Calculation and Visualisation	homepage
	MIDAS	Microarray Data Analysis System	Microarray software suite TM4
	Normalise suite	normalise individual arrays across the entire array or by subgrids, group individual arrays into a project and take specific projects and generate results plots	homepage
	SMA	R-package : Statistics for Microarray Analysis	homepage
	SNOMAD	Standardization and NOrmalization of MicroArray Data	online forms
	tpWY	t-statistics, p-values, and Westfall and Young step-down method	homepage

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Transcriptomics : preprocessing

	Name	Description	Link
	AMIADA	an integrated computer program for organizing, exploring, visualizing, and analyzing microarray data	homepage
	Array File Maker	generates input files for clustering, helps prepare colored figures and Venn diagrams, and can uncover aneuploidy in yeast microarray data.	homepage
	Data processing of time course data	A suite of Excel spreadsheet templates	homepage
	MeV	Multi experiment Viewer
	SAM-software	Supervised learning software for genomic expression data mining	homepage

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Transcriptomics : probe design

	Name	Description	Link
	CAPS marker	description after restriction profiles analysis
	Clone selection
	Degenerate primers design	Degenerate primers based on a set of proteic sequences
	FindExpress	internal primer design on a set of nucleotidic sequences
	Genofrag	Primer design program in two steps, first primer selection then genome fragmentation
	Interactive PCR Primer Design	Part of GeneFischer package
	Microsatellites primers	Microsatellite repeat search with Sputnik and primers design with Primer3
	Oligo Heat Map	an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences	Use Oligo Heat Map
	Oligo search
	Primo	A primer design tool
	Roso	A software to design optimized oligonucleotide probes (size over 25 nucleotides) for microarrays
	Spads	design a GST (Gene-Specific Tag) and a specific primer set for its PCR amplification, on a genomic sequence, knowing the gene structure	Spads webpage
	XXFrag	help the biologist in the creation of Biochips by collecting some fragments coming from the pseudogenome required

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