BioResource Index

Welcome to BioResource Index

BioResource Index is an index of commonly used bioinformatics and systems biology databases and software tools. The index covers resources for the analysis of high-throughput genetic, transcriptional, sequence analysis and proteomic profiling. BioResource Index was developed as part of the StemDB database project, funded by the EU FP7 project Eurosystem.

To learn more about BioResource Index and EuroSyStem, click here.

Recent Updates:

There are currently 548 resources detailed on this site, with 720 references and 550 links detailing them.

Our contributors have entered 3 reviews on these resources.

Name	Description	Type	Platforms	Rating	Last Updated	Links
Manteia	"Manteia is an advanced data mining tool that allows scientists to combine a variety of data and tools in order to adress complex biological questions. To start with Manteia select a tool from the menu above or using the links below. Data can be combined using our query builder or the refine tool as explained in our tutorials. If you don't know where to start, you probably want to look for a particular gene using Molecule search or analyze a list of genes using Batch gene entry. Only a part of Manteia is accessible to the general public at the time being. The full system will be released soon."	Annotation : Ontology : GO : Functional Analysis : Genome Annotation : Data Analysis	Web		April 17, 2012	Manteia
X! P3 (Proteotypic Peptide Profiler)	It should be possible to scan through a set of data, for example an LC/MS/MS run, looking only for the known proteotypic peptides for a particular organism. Finding those proteotypic peptides is enough to know that the protein was present in the original sample. Because there will only be a few proteotypic peptides for a protein, it should be possible to improve both the speed and accuracy of the resultant protein identifications. The X! P3 (Proteotypic Peptide Profiler) project is the first publically available search engine that takes advantage of this idea.	Proteomics	Web, Linux, Source, Download		April 4, 2012	X! P3 Home
X! Hunter	X! Hunter identifies MS Spectra. Rather than predicting spectra from a peptide sequence, it directly compares an input spectrum to a library of spectra that have been confidently assigned to a particular peptide sequence.	Proteomics	Web, Linux, Source, Download		April 4, 2012	X! Hunter Home
TOPP and TOPPAS	TOPP (The OpenMS Proteomics Pipeline) is a pipeline for the analysis of HPLC/MS data. It consists of several small applications that can be chained to create analysis pipelines tailored for a specific problem. The TOPP Pipeline Assistant (TOPPAS), is a graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows	Proteins : Proteomics : Workflow	Windows, Linux, Source, Download		March 30, 2012	TOPP / TOPPAS site
OpenMS	OpenMS is a library of tools for proteomic analysis	Proteomics	Windows, Linux, Source, Download		March 30, 2012	OpenMS Homepage
MSPolygraph	MS Polygraph is a tool for identifying peptides from tandem mass spectrometry data. It uses advanced mathematics and computer science to accurately identify peptides from tandem mass spectrometry data from individual organisms or communities of microbes.	Proteomics	Linux		March 30, 2012	MS-Polygraph MR/MS-Polygraph
OMSSA	OMSSA is an open source search engine for identifying MS/MS peptide spectra.	Proteomics	Web, Linux, Source, Download		March 30, 2012	OMSSA Site
SQID	An Intensity-Incorporated Protein Identification Algorithm for Tandem Mass Spectrometry	Proteomics	Windows, Source, Download		March 30, 2012	SQID Home
X!!Tandem	X!!Tandem is a parallel, high performance version of X!Tandem that has been parallelized via MPI to run on clusters or other non-shared memory multiprocessors running Linux.	Proteins : Proteomics	Linux, Source, Download		March 27, 2012	X!!Tandem Home
X! Tandem	X! Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification.	Proteins : Proteomics	Linux, Source, Download		March 27, 2012	X! Tandem site
InSilico DB	Gene Expression Genomics Database	Database : Gene Annotation : Expression	Web		March 27, 2012	Home Page
Proteome Commons	Proteome Commons is a public proteomics database for annotations and other information linked to the Tranche data repository and to other resources. We provide public access to free, open-source proteomics tools and data.	Proteomics	Web, Download		March 26, 2012	Proteome Commons
Cortex	Cortex is a de novo assembler capable of assembling multiple eukaryotic genomes simultaneously	Genome Assembly	Linux, UNIX, Source, Download		March 4, 2012	Cortex Main Page
YABI	An online research environment for Grid, High Performance and Cloud computing	Tool : Data Format : Genome : Data Analysis : Genetics : Workflow	Web		March 4, 2012	Demo tool
InnateDB	"InnateDB provides a manually-curated knowledgebase of the genes, proteins, and particularly, the interactions and signaling responses involved in mammalian innate immunity. InnateDB incorporates information of the whole human, mouse and bovine interactomes by integrating interaction and pathway information from several of the major publicly available databases but aims to capture an improved coverage of the innate immunity interactome through manual curation." from http://www.innatedb.ca/about.jsp	Database : Interaction	Web		March 1, 2012	InnateDB
GeneMANIA	"GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input."	Tool : Pathway : Interaction : Protein Interaction	Web		March 1, 2012	GeneMANIA
GeneProf	GeneProf is a web-based, graphical software suite that allows users to analyse data produced using next-generation sequencing platforms.	Tool : Integrated Analysis : Next-Generation Sequencing : Stem Cell	Web, Download		January 25, 2012	Home Page
The MEME Suite	Motif-based sequence analysis tools	Tool : Gene Regulation	Web, Download		December 14, 2011	Home Page
Mugen	MUGEN mouse database; animal models of human immunological diseases	Database : Disease	Web		October 19, 2011	Home Page
BioProfiling.de	Analytical web portal for high-throughput cell biology	Tool : Gene Regulation	Web		October 19, 2011	Home Page
Chipster	Chipster brings a powerful collection of data analysis methods within the reach of bioscientists via its intuitive graphical user interface. Users can analyze and integrate different data types such as gene expression, miRNA and aCGH	Tool : Microarray : Expression Analysis : Expression	Java		October 19, 2011	Home Page
AS-ALPS	AS-ALPS (Alternative Splicing-induced ALteration of Protein Structure), is aimed at providing useful information to analyze effect of AS on protein interaction and network through alteration of protein structure	Database : Protein Structure : Splicing	Web		October 16, 2011	Home Page
MEDIE	MEDIE is an intelligent search engine to retrieve biomedical correlations from MEDLINE, based on indexing by Natural Language Processing and Text Mining technique	Database	Web		October 16, 2011	Home Page
EMBRYS	Embryonic Gene Expression Database for Biomedical Research Source	Database : Gene Expression : Expression	Web		October 16, 2011	Home Page
Genome Network Platform	Building a human genome network platform- integrating organically global genome information with data from participants in the genome network	Database : Gene Expression : SNP : Genome Annotation : Proteomics	Web		October 16, 2011	Home Page
InSilicoDb	"InSilico DB is a complete web-based solution for finding and exporting uniformly processed and curated genomics datasets"	Database : Gene Expression : Microarray : Gene Expression Analysis : Expression	Web		October 7, 2011	Home Page
MEME-ChIP	The MEME-ChIP web service is designed to analyze ChIP-seq 'peak regions'--short genomic regions surrounding declared ChIP-seq 'peaks'.	Tool : Next-Generation Sequencing	Web		August 11, 2011	Home Page
MATISSE	MATISSE (Module Analysis via Topology of Interactions and Similarity SEts) is a program for detection of functional modules using interaction networks and expression data.	Tool : Gene Expression : Functional Analysis : Gene Expression Analysis : Protein Interaction	Windows, Linux, Java		August 10, 2011	Home Page
Stemformatics	a portal to a series of public experiments describing mouse and human stem cells and how they differentiate to become mature cells, tissues and organs. You'll find data from leading stem cell laboratories in a format that is easy to search, easy to visualise and easy to export. Log in to the Workbench to run and save your own analyses.	Database : Gene Expression Analysis : Expression Analysis : Stem Cell	Web		July 6, 2011	Homepage
Parkinson DB	Parkinson's disease database	Database : Gene Expression : Disease	Web		June 2, 2011	Home Page
MSigDB	Molecular Signatures Database- A collection of gene sets	Database : Integrated Analysis : Gene Expression Analysis : Expression Analysis : Expression	Web, Download		June 2, 2011	Home Page
BloodExpress	A database of gene expression in mouse haematopoiesis.	Database : Gene Expression : Stem Cell	Web		June 1, 2011	Home Page
ARACNE	ARACNE (Algorithm for the Reconstruction of Accurate Cellular Networks), a novel algorithm, using microarray expression profiles, specifically designed to scale up to the complexity of regulatory networks in mammalian cells	Tool : Network : Systems Biology	Windows, Mac, Linux, Java, Source		June 1, 2011	Home Page
Cluster 3.0	Cluster 3.0 is an enhanced version of Cluster, gene expression clustering software	Tool : Gene Expression : Gene Expression Analysis	Windows, Mac, Linux, UNIX, Source		May 31, 2011	Home Page
MoD Tools	MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes	Tool : Gene Regulation	Web		May 31, 2011	Home Page
Weeder Web (1.4)	A tool for the discovery of transcription factor binding sites in a set of sequences from co-regulated genes	Tool : Gene Regulation	Web		May 31, 2011	Home Page
miRecords	miRecords: an integrated resource for microRNA-target interactions.	Database : RNA	Web		May 31, 2011	Home Page
siDRM	siDRM: An online siRNA design tool	Tool : RNA	Web		May 31, 2011	Home Page
siRecords	Database of experimentally validated mammalian siRNAs with efficacy ratings	Database : RNA	Web		May 31, 2011	Home Page
TargetScan	Search for predicted microRNA targets in mammals	Tool : RNA	Web, Source, Download		May 31, 2011	Home Page
TRED	Transcriptional Regulatory Element Database	Database : Gene Regulation	Web		May 31, 2011	Home Page
Geneious	Complex data such as entire bacterial genomes or human chromosomes can be stored, visualized and analyzed using a single desktop application that unites pipelines and tools to ensure analyses are easily repeatable.	Chromosomal : Tool : Molecular Biology : Sequence Analysis : Functional Analysis : Next-Generation Sequencing : Sequence : Expression Analysis : Data Analysis : Expression : Multiple Sequence Alignment	Windows, Mac, Linux		May 31, 2011	Home Page
GUDMap	The GenitoUrinary Development Molecular Anatomy Project	Gene Expression : Integrated Analysis : Gene Expression Analysis : Image : Expression Analysis : Expression	Web		May 31, 2011	Home Page
BioEdit	Biological Sequence Editor	Tool : Sequence Analysis : Sequence	Windows		May 25, 2011	Home Page
Eurexpress	Transcriptome-wide acquisition of expression patterns chiefly by means of in situ hybridization (ISH) with non-radioactive probes and will use this data to establish a web-linked, interactive digital transcriptome atlas of embryonic mouse.	Database : Gene Expression : Expression	Web		May 22, 2011	Home Page
Human Erythroblast Maturation (HEM) Database	Database of global gene expression analysis of human erythroid progenitors	Database : Expression Analysis : Stem Cell : Expression	Web		May 18, 2011	Home Page
GeneXpress	A visualization and analysis tool for gene expression data, integrating clustering, gene annotation, and sequence information.	Tool : Gene Expression Analysis : Expression Analysis	Java		May 17, 2011	Home Page
FIRE	A motif discovery and characterization program based on mutual information.	Tool : Sequence Analysis	Web		May 17, 2011	Home Page
ChARM	Detection of aneuploidies in array CGH and gene expression microarray data	Chromosomal : Tool : aCGH : Gene Expression Analysis	Download		May 17, 2011	Home Page
CellTracer	Cell Tracking software	Tool : Systems Biology	Windows		May 17, 2011	Home Page
KEA	Provides users with the ability to link lists of mammalian proteins/genes with the kinases that phosphorylate them.	Tool : Functional Analysis : Systems Biology	Web		May 17, 2011	Home Page
Lists2Networks	Integrated analysis of gene/protein lists	Tool : Systems Biology	Web		May 17, 2011	Home Page
snavi	Desktop Application for Analysis and Visualization of Large-Scale Cell Signaling Networks	Tool : Systems Biology	Windows, Source		May 17, 2011	Home Page
AVIS	AJAX viewer of interactive signaling networks	Tool : Systems Biology	Source		May 17, 2011	Home Page
BioModels Database	BioModels Database is a repository of peer-reviewed, published, computational models.	Database : Systems Biology	Web		May 17, 2011	Home Page
The Database of Quantitative Cellular Signaling	A repository of models of signaling pathways.	Database : Systems Biology	Web		May 17, 2011	Home Page
Jaspar	Database of transcription factor binding profiles	Database : Gene Regulation	Web, Download		May 11, 2011	Home Page
Galaxy	Genome Annotation & Analysis System	Database : Genome Annotation	Web		May 2, 2011	Home Page
Mayday SeaSight	Next-generation sequencing analysis for the Mayday software suite	Sequence Analysis : Next-Generation Sequencing : Sequence	Java		February 10, 2011	Home Page
MIT IGV	The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets	Tool : Genomic Annotation : Next-Generation Sequencing	Java		February 8, 2011	Home Page
Savant	Savant: genome browser for high-throughput sequencing data.	Sequence Analysis : Next-Generation Sequencing : Sequence	Web		February 7, 2011	Home Page
Modmine	The modENCODE project aims to identify all sequence-based functional elements in the C. elegans and D. melanogaster genomes. modMine is an integrated web resource of data & tools to browse and search modENCODE data.	Database : Gene Expression : Annotation : Sequence Analysis : Functional Analysis : Gene Annotation : Genomic Annotation : Gene Expression Analysis : Next-Generation Sequencing	Web		February 7, 2011	Home Page
Ruffus	Ruffus is a lightweight python module to run computational pipelines.	Tool : Workflow	Python		February 7, 2011	Home Page
GEDS	Gene Expression Data Simulator	Gene Expression : Gene Expression Analysis	Web		February 7, 2011	Home Page
DESeq	DESeq is an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression	Tool : Sequence Analysis : Next-Generation Sequencing : Sequence	Windows, Mac, Source		February 7, 2011	Home Page
Circos	Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions.	Chromosomal : Tool	Perl, Windows, Mac, Linux, UNIX, Source		February 3, 2011	Home Page
RACE	Collection of web tools designed to assist with the analysis of DNA microarray data and results.	Tool : Gene Expression : Gene Expression Analysis	Web		February 2, 2011	Home Page
MAQ	Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines	Tool : Sequence Analysis : Next-Generation Sequencing : Sequence	Source		January 25, 2011	Home Page
Webgestalt	WebGestalt is a "WEB-based GEne SeT AnaLysis Toolkit". It is designed for functional genomic, proteomic and large-scale genetic studies from which large number of gene lists...	Tool : Functional Analysis	Web		January 23, 2011	Home Page
Vmatch	A software tool for efficiently solving large scale sequence matching tasks.	Tool : Next-Generation Sequencing	Mac, Linux, UNIX		January 22, 2011	Home Page
Bowtie	Bowtie is an ultrafast, memory-efficient short read aligner	Tool : Sequence Analysis : Next-Generation Sequencing : Sequence	Windows, Mac, Linux, Source		January 20, 2011	Home Page
caBIG	Integrated informatics portal	Database : Tool : Cancer	Web		January 20, 2011	Home Page
BRB-ArrayTools	BRB-ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data	Microarray : Expression Analysis : Expression	Windows		January 20, 2011	Home Page
GeneCluster 2.0	GeneCluster 2.0 expands the data analysis capabilities of GeneCluster 1.0 sample classification tool by adding supervised classification, gene selection and permutation test methods. It includes algorithms for building and testing supervised models using weighted voting (WV) and k-nearest neighbors (KNN) algorithms	Microarray : Expression Analysis : Expression	Windows, Mac, Linux		January 19, 2011	Home Page
RMAexpress	RMAExpress is a standalone GUI program for Windows (and Linux) to compute gene expression summary values for Affymetrix Genechip® data using the Robust Multichip Average expression summary	Microarray : Data Analysis	Windows, Linux		January 19, 2011	Home Page
dChip	Dchip (D-Chip), Analysis and visualization of gene expression and SNP microarrays	Tool : Microarray : SNP : Expression Analysis : Expression	Windows, Mac, Linux, Source		January 19, 2011	Home Page
Cyber-t	Cyber-T is a statistics program with a web interface that can be conveniently used on high-dimensional array data for the identification of statistically significant differentially expressed genes	Tool : Gene Expression : Microarray : Gene Expression Analysis	Web		January 19, 2011	Home Page
Weka	Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes.	Tool : Expression Analysis	Windows, Mac, Linux, Java, Source		January 19, 2011	Home Page
BioWeka	BioWeka is an extension library to the data mining framework Weka for knowledge discovery and data analysis tasks in biology, biochemistry and bioinformatics.	Tool : Gene Expression : Sequence Analysis : Gene Expression Analysis	Java		January 19, 2011	Home Page
GenePattern	GenePattern is a powerful genomic analysis platform that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.	Tool : Gene Expression : Functional Analysis : SNP : Gene Expression Analysis : Expression Analysis : Data Analysis	Web, Java, Source		January 19, 2011	Home Page
Integrative Genome Viewer	The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets	Tool : Integrated Analysis : Genome : Genome Annotation : Expression : Epigenomics	Windows, Mac, Linux, Java, Source		January 17, 2011	Home Page
NextBio	NextBio Basic provides access to a curated, correlated database of public data; integrated literature, clinical trials, and scientific news	Database : Gene Expression : Integrated Analysis : Disease : Proteomics : Epigenomics	Web, Commercial		January 13, 2011	Home Page
SCLD	A stem cell lineage database	Database : Stem Cell	Web		January 7, 2011	Home Page
NCBI Epigenomics	A public resource for exploring epigenomic data sets	Database : Next-Generation Sequencing : Epigenomics	Web		January 7, 2011	Home Page
GEO	Gene Expression Omnibus: a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted	Database : Gene Expression : Microarray	Web		January 7, 2011	Home Page
UCSC	The UCSC site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides a portal to the ENCODE project.	Database : Genome Annotation	Web		January 7, 2011	Home Page
IKMC	The IKMC database and web portal (www.knockoutmouse.org) serves as the central public web site for IKMC data and facilitates the coordination and prioritization of work within the International Knockout Mouse Consortium	Database : Genetics	Web		January 7, 2011	Home Page
GXD	The Gene Expression Database (GXD) is a community resource for gene expression information from the laboratory mouse	Database : Gene Expression	Web		January 7, 2011	Home Page
Ensembl	The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online	Database : Genome Annotation	Web		January 7, 2011	Home Page
miRBase	miRBase is the primary online repository for all microRNA sequences and annotation.	RNA : Sequence	Web		January 7, 2011	Home Page
Reactome	Reactome - a curated knowledgebase of biological pathways	Database : Network Analysis : Pathway	Web		January 7, 2011	Home Page
BioGRID	BioGRID is an online interaction repository with data compiled through comprehensive curation effort	Database : Interaction	Web		January 7, 2011	Home Page
STRING	STRING - Known and Predicted Protein-Protein Interactions	Tool : Protein Interaction	Web		January 7, 2011	Home Page
Entrez Gene	Entrez Gene is a searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer	Database : Gene Annotation	Web		January 7, 2011	Home Page
Genbank	GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms.	Database : Sequence	Web		January 7, 2011	Home Page
ENA	ENA-European Nucleotide Archive provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation	Database : Next-Generation Sequencing : Sequence	Web		January 7, 2011	Home Page
SRA	SRA- next-generation sequence archive	Tool : Next-Generation Sequencing : Sequence	Web		January 7, 2011	Home Page
DRA	DDBJ Sequence Read Archive (DRA) is an archive database for output data generated by next-generation sequencing machines including Roche 454 GS System®, Illumina Genome Analyzer®, Applied Biosystems SOLiD® System, and others.	Database : Next-Generation Sequencing : Sequence	Web		January 7, 2011	Home Page
NSDC	Under the International Nucleotide Sequence Database Collaboration globally comprehensive public domain nucleotide sequence is captured, preserved and presented.	Next-Generation Sequencing : Sequence	Web		January 7, 2011	Home Page
MACS	Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer	Tool : Next-Generation Sequencing	Python		January 7, 2011	Home Page
ENCODEdb	This portal provides users a single, unified point-of-access to data generated by the ENCODE Consortium, regardless of which public database the primary data is housed in	Database	Web		January 6, 2011	Home Page
Epigraph	EpiGRAPH is a software for genome and epigenome analysis	Tool : Sequence Analysis : Next-Generation Sequencing	Web		January 6, 2011	Home Page
GENIO/logo	RNA/DNA & Amino Acid Sequence Logos	Tool : RNA : Protein Sequence : Sequence	Web		December 22, 2010	Home Page
pLogo	Protein Sequence Logos using Relative Entropy	Tool : Protein Sequence : Sequence	Web, Source		December 22, 2010	Home Page
WebLogo	A web-based application for the generation of sequence logos	Tool : Sequence	Web, Source		December 22, 2010	Home Page
SeqLogo	seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo	Tool : Sequence	Windows, Mac, Source		December 22, 2010	Home Page
SeeGraph	SeeGraph is a package for the interactive visualization and analysis of graphs	Tool	Windows, Linux		December 22, 2010	Home Page
Trans-Proteomic Pipeline	The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics	Tool : Proteomics : Data Analysis	Windows, Mac, Linux, Source		December 21, 2010	Home Page
Bioinformatics Resource Manager	Bioinformatics Resource Manager automates multidisciplinary data mining processes used for high-throughput molecular profiling.	Tool : Integrated Analysis : Expression Analysis	Java		December 20, 2010	Home Page
Ontological Discovery Environment	The Ontological Discovery Environment allows users to integrate phenotype centered gene sets across species, tissue and experimental platform	Database : Tool : Microarray : Integrated Analysis : Gene Expression Analysis : Data Analysis	Web		December 20, 2010	Home Page
SBEAMS	Systems Biology Experiment Analysis Management System (SBEAMS), enables MIAME-compliant storage, management, analysis, and integration of high-throughput genomic expression dat	Database : Gene Expression : Microarray : Proteomics : Expression	Web, Source		December 20, 2010	Home Page
BLASTO	BLAST on Orthologous groups (BLASTO), a modified BLAST tool for searching orthologous group data	Tool : Sequence Analysis : Sequence	Web		December 20, 2010	Home Page
edgeR	edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.	Tool : Sequence Analysis : Next-Generation Sequencing	Windows, Mac, Linux, Source, Download		December 16, 2010	Home Page
iScMiD	Integrated Stem Cell Molecular Interaction Database (iScMiD)	Database : Stem Cell	Web, Download		December 14, 2010	Home Page
STITCH	STITCH is a resource to explore known and predicted interactions of chemicals and proteins	Proteins : Protein Interaction	Web		December 14, 2010	Home Page
CellProfiler	CellProfiler is designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically	Tool : Image : Image Analysis	Windows, Mac, Linux, Source		November 25, 2010	Home Page
Cell Profiler Analyst	CellProfiler Analyst is free open-source software for exploring and analyzing large, high-dimensional image-derived data	Image : Image Analysis	Windows, Mac, Linux, Source		November 25, 2010	Home Page
Embryonic stem cells database (ESCDb)	Gathers chromatin immunoprecipitation on chip and sequencing data together with perturbation experiments conducted on both human and mouse (ESC) and embryonic carcinoma cells (EC)	Database : Stem Cell	Web		November 25, 2010	Home Page
The KTH-Package	A collection of tools to make microarray analysis easier	Tool : Gene Expression : Microarray : Gene Expression Analysis	Windows, Mac		October 25, 2010	Home Page
GATE	Grid Analysis of Time Series Data	Tool : Gene Expression : Microarray : Gene Expression Analysis : Stem Cell	Windows, Mac, Linux, Java		October 25, 2010	Home Page
CARMAWeb	A comprehensive R- and Bioconductor-based web service for microarray data analysis	Tool : Gene Expression : Microarray : Functional Analysis : Gene Expression Analysis : Data Analysis	Web		October 25, 2010	Home Page
The Ellington Lab Aptamer Database	Aptamers are DNA or RNA molecules select that have been identified by their ability to bind other molecules	Database : RNA : Sequence	Web		October 19, 2010	Home Page
SKY/M-FISH and CGH Database	A database for sharing and comparing molecular cytogenetics data	Database : Chromosomal : Cancer	Web		October 19, 2010	Home Page
Telomerase Database	A web-based database to study the function, structure and evolution of telomerase ribonuclearprotein	Database : Genomic Annotation : Protein Structure	Web		October 19, 2010	Home Page
R-GSEA	Gene set enrichment analysis with R.	Tool : Functional Analysis	Source, Download		October 19, 2010	Download Page
GSEA	Gene Set Enrichment Analysis-	Tool : Functional Analysis : Expression Analysis	Java, Source		October 19, 2010	Home Page
ProSplicer	Alternative splicing database produced from variant protein and gene expression patterns	Database : Splicing	Web		October 19, 2010	Home Page
Home Page	Human Transcriptome Database for Alternative Splicing	Database : Splicing	Web		October 19, 2010	Home Page
ASSP	Alternative Splice Site Prediction	Tool : Sequence Analysis : Splicing	Web		October 19, 2010	Home Page
ASTD	Alternative Splicing and Transcipt Diversity database	Database : Sequence : Splicing	Web, Download		October 19, 2010	Home Page
ScanPS Web Server	SCANPS performs iterative profile searching similar to PSI-BLAST but with full dynamic programing on each cycle and on-the-fly estimation of significance	Tool : Sequence Analysis : Protein Sequence	Web		October 15, 2010	Home Page
PASS2	PASS2 contains alignments of protein structures at the superfamily level	Database : Proteins : Protein Sequence : Protein Structure : Sequence	Web		October 15, 2010	PASS2
UniVec	A database of cloning vector nucleic acid sequences that can be used to identify segments of sequence that of vector origin	Tool : Sequence Analysis	Web		October 15, 2010	Home Page
AceDB	AceDB is a flexible database designed to store genomic data	Database : Genome : Genomic Annotation	Windows, Mac, Linux, UNIX, Source, Download		October 15, 2010	Home Page
Stem Cell Mesa	Stem Cell Microarray Data Server	Database : Gene Expression : Stem Cell : Expression	Web		September 16, 2010	Home Page
Tablet	Tablet?next generation sequence assembly visualization	Tool : Sequence Analysis : Next-Generation Sequencing : Sequence : Genome Assembly	Windows, Mac, Linux, Java, UNIX		August 17, 2010	Home Page
WWW Signal Scan	Web version of SignalScan, a computer program that scans DNA sequences for eukaryotic transcriptional elements	Tool : Gene Regulation : Sequence Analysis : Sequence	Web		August 6, 2010	Home Page
ConSequenceS	This is a method for searching and aligning databases of consensus sequences	Tool : Sequence Analysis : Sequence	Web		August 6, 2010	Home Page
Exalign	Exalign is a tool that performs alignments of gene exonic structures.	Tool : Sequence Analysis : Gene Annotation : Gene Prediction : Sequence	Web		August 6, 2010	Home Page
SECISaln	SECISaln will predict a eukaryotic [selenocysteine] SECIS element in a nucleotide sequence	Tool : Protein Annotation : Proteins : Protein Signatures	Web		August 6, 2010	Home Page
FSA	Fast statistical alignment of biological sequences	Tool : Sequence Analysis : Sequence	Web		August 6, 2010	Home Page
PubMed	PubMed comprises approximately 20 million citations for biomedical literature from MEDLINE, life science journals, and online books. PubMed citations and abstracts include the fields of medicine, nursing, dentistry, veterinary medicine, the health care system, and preclinical sciences. PubMed also provides access to additional relevant Web sites and links to the other NCBI molecular biology resources. PubMed is a free resource that is developed and maintained by the National Center for Biotechnology Information (NCBI), at the U.S. National Library of Medicine (NLM), located at the National Institutes of Health (NIH).	Database : Literature Mining	Web		August 6, 2010	Homepage
Venny	Venny is a simple web-based tool for creating Venn diagrams of up to four different lists. Venny automatically calculates the overlaps for all possible permutations of the given datasets (say, lists of gene symbols or probe ID's).	Tool	Web		August 6, 2010	Homepage
SWISS-MODEL Repository	The SWISS-MODEL Repository is a database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.	Database	Web		August 6, 2010	Home Page
CrossChip	A microarray analysis often involves comparing data across different platforms. Unfortunately, significant differences exist among these platforms and data cannot be combined directly	Integrated Analysis	Java		August 6, 2010	Home Page
iHOP	Information Hyperlinked over Proteins. A gene network for navigating the literature	Database : Protein Annotation : Literature Mining	Web		August 6, 2010	Home Page
WebGestalt	WebGestalt is a "WEB-based GEne SeT AnaLysis Toolkit". WebGestalt incorporates information from different public resources and provides an easy way for biologists to make sense out of large sets of genes	Chromosomal : Tool : Gene Expression	Web		August 6, 2010	Home Page
CisGenome	An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.	Tool : Next-Generation Sequencing	Windows, Mac, Linux, Source	(1 review)	June 24, 2010	Home Page
R	Software enviroment for statistical calculations and graphics	Tool	Windows, Mac, UNIX	(1 review)	January 7, 2011	Home Page
Bioconductor	Central bioinformatics project that runs within R	Tool : Data Analysis	Windows, Mac, Linux, Source	(1 review)	June 24, 2010	Home Page
Praline	PRALINE is a multiple sequence alignment program with many options to optimise the information for each of the input sequences; e.g. homology-extended alignment, predicted secondary structure and/or transmembrane structure information.	Database : Tool : Sequence Analysis	Web		August 6, 2010	Home Page
PlasMapper	The PlasMapper server automatically generates and annotates plasmid maps using only the plasmid DNA sequence as input.	Tool : Molecular Biology : Sequence Analysis	Web, Source, Download		August 6, 2010	Home Page
WebCutter 2.0	Restriction map prediction software	Tool : Molecular Biology : Sequence Analysis	Web		August 6, 2010	Home Page
PROMALS3D	PROMALS3D constructs alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints	Database : Proteins : Sequence Analysis : Functional Analysis : Gene Annotation : Protein Sequence	Web		August 6, 2010	Home Page
PairsDB	PairsDB is a collection of protein sequences and the BLAST and PSI-BLAST alignments between them	Database : Sequence Analysis	Web		August 6, 2010	Home Page
Rankprop	A web server for protein remote homology detection	Proteins : Sequence Analysis : Data Format	Web, Source		August 6, 2010	Home Page
PDBSum	PDBsum provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB).	Database : Proteins : Protein Structure	Web		August 6, 2010	Home Page
Annotation-Modules	A tool for finding significant combinations of multisource annotations in gene lists	Annotation	Web		August 6, 2010	Home Page
AutoSOME	AutoSOME is a new unsupervised multidimensional clustering method for identifying clusters of diverse shapes and sizes from large numerical datasets	Gene Expression Analysis : Expression Analysis : Data Analysis	Java, Download		August 6, 2010	Home Page
GENtle	GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more	Molecular Biology	Windows, Mac, Linux, Source		August 5, 2010	Home Page
DAVID	Annotation, visualisation and functional enrichment and functional discovery in sets of genes	Tool : Functional Analysis	Web		August 3, 2010	Home Page
Pfam	The Pfam protein families database.	Database : Protein Annotation : Protein Signatures	Web		July 28, 2010	Home Page
Mayday	Mayday is a workbench for visualization, analysis and storage of microarray data	Gene Expression : Microarray : Integrated Analysis : Gene Expression Analysis : Expression Analysis	Java		July 27, 2010	Home Page
ProfCom	ProfCom automatically generates statistically valid hypotheses / biological models from gene or protein lists supplied by the user. This knowledge can help to improve your understanding of genetic mechanisms involved in biological phenomena under study.	Tool : Modelling	Web		June 29, 2010	Home Page
GeneCards	GeneCards is a searchable, integrated, database of human genes that provides concise genomic, transcriptomic, genetic, proteomic, functional and disease related information on all known and predicted human genes	Database : Gene Annotation	Web		June 25, 2010	Home Page
caGEDA	A web application for the integrated analysis of global gene expression patterns in cancer	Tool : Integrated Analysis : Disease : Cancer	Web		June 25, 2010	Home Page
Cellminer	CellMiner? is a web application that facilitates systems biology through the retreival and integration of the various molecular data sets	Integrated Analysis	Web		June 25, 2010	Home Page
LefMiner	LeFEMiner determines which sets of functionally related genes (ie. gene categories or ensembles) are most biologically related to the observed biology or state of the samples	Tool : Functional Analysis	Windows, Mac, Linux, Source		June 24, 2010	Home Page
GlobalTest	Testing groups of covariates/features for association with a response variable with application to gene set testing	Tool : Functional Analysis	Windows, Mac, Linux, Source		June 24, 2010	Home Page
Apex Proteomics	The APEX Quantitative Proteomics Tool, is a free and open source Java implementation of the APEX technique for the quantitation of proteins based on standard LC- MS/MS proteomics data (Lu et al., Nature Biotech., 25(1):117-124, 2007).	Tool : Proteomics	Windows, Mac, Linux, Source		June 24, 2010	Home Page
Genesis	A platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments.	Tool : Gene Expression : Microarray : Integrated Analysis	Windows, Linux, Java		June 24, 2010	Home Page
Magnolia	Magnolia provides PFGRC array users with a series of intelligent entry form to collect the information or parameters of experiment, bio-source, sample, probe, slide, scan, expression, and normalization, which isMIAME compliant	Tool : Microarray : Expression	Windows		June 24, 2010	Home Page
Katsura	The Katsura tool is a free open source Java application designed to overlay gene expression data, comparative genomics data, or quantitative shotgun proteomics data onto metabolic pathway	Chromosomal : Tool : aCGH : Gene Expression : Microarray : Network Analysis : Pathway	Windows, Mac, Linux, Source		June 24, 2010	Home Page
GeneTrack	GeneTrack is a bioinformatics software package for storing, querying and visualizing interval oriented data	Chromosomal : Tool	Python		June 24, 2010	Home Page
AMOS	Manipulation of input and output files related to whole-genome shotgun assembly.	Tool : Genome Assembly	UNIX		June 24, 2010	Home Page
Celera Assembler	Celera Assembler can reconstruct long sequences of genomic DNA given the fragmentary data produced by whole-genome shotgun sequencing	Tool : Genome Assembly	UNIX		June 24, 2010	Home Page
Elvira	High throughput assembly of amplicon reads for virus-sized genomes	Tool : Genome Assembly			June 24, 2010
Flexarray	FlexArray is a Microsoft Windows software package for statistical analysis of microarray expression data	Tool : Gene Expression : Microarray	Windows		June 24, 2010	Home Page
Ginkgo	Ginkgo is a spotted microarray data pre-processing platform featuring analysis functionalities for CGH and expression data.	Chromosomal : Tool : aCGH : Gene Expression : Microarray	Windows, Linux, Source		June 24, 2010	Home Page
RMA Express	RMAExpress is a standalone GUI program for Windows (and Linux) to compute gene expression summary values for Affymetrix Genechip® data using the Robust Multichip Average expression summary and to carry out quality assessment using probe-level met	Tool : Gene Expression : Microarray	Windows, Linux		June 24, 2010	Home Page
SiSA	SISA allows you to do statistical analysis directly on the Interne	Tool : Data Analysis	Web		June 24, 2010	Home Page
TRANSFAC	BLK TRANSFAC is an internationally unique knowledgebase containing data on transcription factors, their experimentally-proven binding sites, and regulated genes	Tool : Gene Regulation	Web, Commercial, Download		June 24, 2010	Home Page
Limma	Linear models for gene expression. Microarray differential gene indentification package	Tool : Gene Expression : Microarray	Windows, Mac, UNIX		June 24, 2010	Home Page
MeV	Multiexperiment Viewer Analysis visualisation and mining of genomic data	Tool : Gene Expression : Microarray	Windows, Mac, Linux		June 24, 2010	Home Page
GeneNetwork	GeneNetwork consists of linked resources and analysis tools for systems genetics	Tool : Systems Biology : Genetics	Web		June 24, 2010	Home Page
Gillespie Simulator	A graphical user interface for simulations of stochastic network models and statistical analysis on the results.	Tool : Modelling	Windows, Mac, Linux		June 24, 2010	Home Page
ENFIN	A Joint Research Program covering the fields of Discrete Function Prediction, Network Reconstruction, Systems-Level Modeling	Tool : Modelling : Network	Web		June 24, 2010	Home Page
XPPAUT	Provides numerical solvers and analysis tools for models described by discrete and continuous equations.	Tool : Modelling	Windows, Mac, Linux, Source		June 24, 2010	Home Page
Beta Cell Biology Consortium	Beta Cell Genomics: The genomics section contains detailed information about genes, mRNA expression studies, and ChIP studies.	Database : Stem Cell	Web		June 24, 2010	Home Page
SCDb	SCDB- the stem cell database	Database : Stem Cell	Web		June 24, 2010	Home Page
ASTD	Alternative Splicing and Transcript Diversity database	Tool : Sequence Analysis	Web		June 24, 2010	Home Page
AltAnalyze	AltAnalyze works with conventional microarrays (3' arrays) but also includes specialized functions for exon (Affymetrix Exon 1.0 and Gene 1.0) and junction arrays to identify predicted alternative splicing or alternative promoter change	Tool : Expression Analysis	Windows, Mac, Linux, Source		June 24, 2010	Home Page
ASPIC	ASPic (Alternative Splicing Prediction) is a web-based tool to detect the exon-intron structure of a gene by comparing its genomic sequence to the related cluster of EST	Tool : Sequence Analysis	Web		June 24, 2010	Home Page
Systems Biology Workbench	SBW is a framework including different software packages for network modelling, analysis, visualization and data manipulation.	Tool : Modelling : Network Analysis	Windows, Mac, Linux		June 24, 2010	Home Page
CASCAD	CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences.	Tool : SNP	Web		June 24, 2010	Home Page
SNPselector	SNPselector: a web tool for selecting SNPs for genetic association studies	Tool : SNP	Web		June 24, 2010	Home Page
SNPeffect	Molecular phenotyping of human SNPs and disease mutations	Tool : SNP	Web		June 24, 2010	Home Page
SNPmasker	SNPmasker 1.0 is a program to mask all SNPs in given sequence using information of dbSNP.	Tool : SNP	Web		June 24, 2010	Home Page
FeatureScam	Searching for sequence similarity by comparing physico-chemical properties of DNA	Database : Sequence	Web		June 24, 2010	Home Page
TraceTuner		Tool : Molecular Biology			June 24, 2010	Home Page
Sky, M-FISH and aCGH database	aCGH and Sky and m-fish database	Database : Genomic Aberration : Chromosomal : Disease : Cancer	Web		June 24, 2010	Home Page
ACUTS	ACUTS: compilation of Ancient Conserved UnTranslated Sequences	Database : Sequence	Web		June 24, 2010	Home Page
dbSTS	dbSTS is an NCBI resource that contains sequence data for short genomic landmark sequences or Sequence Tagged Sites (sequences unique in the genome)	Database : Sequence	Web		June 24, 2010	Home Page
dbEST	dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms	Database : Sequence	Web		June 24, 2010	Home Page
DDBJ	DNA Databank of Japan	Database : Sequence	Web		June 24, 2010	Home Page
EMBL	The EMBL Nucleotide Sequence Database (also known as EMBL-Bank) constitutes Europe's primary nucleotide sequence resource	Database : Sequence	Web		June 24, 2010	Home Page
Lucy2	A graphical tool for cleaning data produced by automated Sanger DNA sequencers prior to sequence assembly and other downstream uses.	Tool : Sequence Analysis	Windows, Mac, Linux		June 24, 2010	Home Page
Lucy	A tool for cleaning data produced by automated Sanger DNA sequencers prior to sequence assembly and other downstream uses.	Tool : Sequence Analysis	UNIX		June 24, 2010	Home Page
TIGR Assembler	Enabled the first published whole-genome assembly of a free-living organism in 1995. Last revised in 2003.	Tool : Sequence Analysis			June 24, 2010
GenScan (MIT)	Identification of complete gene structures in genomic DNA	Tool : Sequence Analysis	Web, Download		June 24, 2010	Home Page
NCBI Genome Workbench	NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data	Tool : Sequence Analysis	Windows, Mac, Linux		June 24, 2010	Home Page
Lasergene	Lasergene is a comprehensive DNA and protein sequence analysis software suite comprised of seven applications which include functions ranging from sequence assembly and SNP detection, to automated virtual cloning and primer design.	Tool : Sequence Analysis	Windows, Mac, Commercial		June 24, 2010	Home Page
W2H	W2H is a free WWW interface to sequence analysis software tools like the GCG-Package (Genetic Computer Group), EMBOSS (European Molecular Biology Open Software Suite) or to derived services (such as HUSAR, Heidelberg Unix Sequence Analysis Resources).	Tool : Sequence Analysis	Web		June 24, 2010	Home Page
Repeat Masker	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences	Tool : Sequence Analysis	Web, Download		June 24, 2010	Home Page
Emboss Explorer	EMBOSS explorer is a web-based graphical user interface to the EMBOSS suite of bioinformatics tools. It is exceedingly simple to install, configure, maintain and use	Tool : Sequence Analysis	Web, Download		June 24, 2010	Home Page
SRS@EBI	Sequence Integration and Analysis Service @EBI	Tool : Sequence Analysis	Web		June 24, 2010	Home Page
Blat	BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments	Tool : Sequence Analysis	Windows, Mac, Linux, Source		June 24, 2010	Home Page
EMBOSS	Sequence analysis suite	Tool : Sequence Analysis	Windows, Mac, Linux, Source		June 24, 2010	Home Page
Jemboss	A graphical viewer for EMBOSS	Tool : Sequence Analysis	Java		June 24, 2010	Home Page
Blast	Sequence searching and alignment tool	Tool : Sequence Analysis	Web, Windows, Mac, Linux		June 24, 2010	Home Page
RNAmod db	A comprehensive listing of post-transcriptionally modified nucleosides from RNA	Database : RNA	Web		June 24, 2010	Home Page
Jarnac	Jarnac is a language for modelling and manipulating network models.	Tool : Modelling	Windows, Mac, Linux		June 24, 2010	Home Page
tRNAdb	tRNAdb 2009 is the new version of "Compilation of tRNA sequences and tRNA genes".	Database : RNA	Web		June 24, 2010	Home Page
Biocatalogue	The BioCatalogue: providing a curated catalogue of Life Science Web Services	Database : Tool : Integrated Analysis	Web		June 24, 2010	Home Page
CellDesigner	CellDesignerTM: A modeling tool of biochemical networks	Tool : Network Analysis : Gene Regulation	Java		June 24, 2010	Home Page
Re1db	The RE1db project has sought to use bioinformatic techniques to help predict genes that are regulated by the repressor element 1(RE1)/RE1 silencing transcription factor (REST) system	Tool : Gene Regulation	Web		June 24, 2010	Home Page
Carrie	CARRIE takes two condition microarray data and applies promoter analysis to infer the stimulated/repressed transcriptional regulatory network.	Tool : Network Analysis : Gene Regulation : Sequence Analysis	Web		June 24, 2010
CompareProspector	CompareProspector conserved regulatory motif discovery package	Tool : Gene Regulation : Sequence Analysis	Web		June 24, 2010	Home Page
CMA	Composite Module Analyst: Defining promoter models based on the composition of transcription factor binding sites and their pairs.	Tool : Gene Regulation : Sequence Analysis	Web		June 24, 2010	Home Page
Bioprospector	Discover conserved motifs in upstream regulatory regions of co-expressed genes	Tool : Gene Regulation : Sequence Analysis	Web		June 24, 2010	Home Page
AffyProbeMiner	Generate a collection of complete coding sequences and rtegroup Affymetrix probes	Database : Microarray : Annotation	Web		June 24, 2010	Home Page
GlycoSuiteDB	Glycoproteomics made easier	Database : Proteomics	Web		June 24, 2010	Home Page
MPDB	Membrane Protein Databank	Database : Proteomics	Web		June 24, 2010	Home Page
WORLD-2DPAGE Repository	A public repository, standards compliant, for proteomics image data published in the literature	Database : Proteomics	Web		June 24, 2010	Home Page
MIAPEGelDB	MIAPEGelDB is intended to help end-users to write such MIAPE documents, through a self-documenting web interface The MIAPE documents specifies the minimum information to report when describing or publishing a proteomics experiment.	Database : Proteomics	Web		June 24, 2010	Home Page
CROPPER	A Fully Automated Software for the Confident Identification of Human Peptides from Tandem Mass Spectra	Database : Proteomics	Web		June 24, 2010	Home Page
VisANT	VisANT: an online visualization and analysis tool for biological interaction data.	Database : Interaction	Java		June 24, 2010	Home Page
MAPU 2.0	MAPU 2.0: high-accuracy proteomes mapped to genomes	Database : Proteomics	Web		June 24, 2010	Home Page
MDscan	A Fast and Accurate Motif Finding Algorithm With Applications To Chromatin Immunoprecipitation Microarray Experiments	Tool : Gene Regulation : Sequence Analysis	Web		June 24, 2010	Home Page
ModBase	MODBASE is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure.	Database : Protein Structure	Web		June 24, 2010	Home Page
SCOP	The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known.	Database : Protein Structure	Web		June 24, 2010	Home Page
PDBTM	Transmembrane protein selection of the Protein Data Bank (PDB)	Database : Protein Structure	Web		June 24, 2010	Home Page
ProSas	The ProSAS (Protein Structure and Alternative Splicing) database provides a unified resource to analyze the effects of alternative splicing events on the structure of the resulting protein isoforms	Database : Protein Structure	Web		June 24, 2010	Home Page
wwPDB	The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data.	Database : Protein Structure	Web		June 24, 2010	Home Page
DisProt	DisProt: the Database of Disordered Proteins	Database : Protein Structure	Web		June 24, 2010	Home Page
MutaProt	Comparison of PDB files which differ by point mutations	Database : Protein Structure	Web		June 24, 2010	Home Page
HSSP	The HSSP database is a database of homology-derived secondary structure of proteins	Database : Protein Structure	Web		June 24, 2010	Home Page
CSD	The world repository of small molecule crystal structures	Database : Protein Structure	Web		June 24, 2010	Home Page
CN3D	Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service	Database : Protein Structure	Windows, Mac, UNIX		June 24, 2010	Home Page
Molecules to Go	NCBI search tool	Database : Protein Structure	Web		June 24, 2010	Home Page
SBASE	SBASE is a collection of protein domain sequences collected from the literature, from protein sequence databases and from genomic databases	Database : Protein Signatures	Web		June 24, 2010	Home Page
Swiss-Pdb Viewer	Load and displaymolecular structures	Database : Protein Structure	Windows, Mac		June 24, 2010	Home Page
ProDom	ProDom is a comprehensive set of protein domain families automatically generated from the UniProt Knowledge Data	Database : Protein Signatures	Web		June 24, 2010	Home Page
PRINTS	PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family; its diagnostic power is refined by iterative scanning of a SWISS-PROT/TrEMBL composite	Database : Protein Signatures	Web		June 24, 2010	Home Page
Panther	The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a resource that classifies genes by their functions	Database : Protein Signatures	Web		June 24, 2010	Home Page
Gene3d	Gene3D: modelling protein structure, function and evolution.	Database : Protein Signatures			June 24, 2010	Home Page Home Page Home Page Home Page Home Page Home Page Home Page
cath	CATH is a manually curated classification of protein domain structures	Database : Protein Signatures	Web		June 24, 2010	Home Page
BLOCKS	Blocks are ungapped multiple alignments of segments of related protein sequences that correspond to the most conserved regions of proteins.	Database : Protein Signatures	Web		June 24, 2010	Home Page
PROSITE	PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them	Database : Protein Signatures	Web		June 24, 2010	Home Page
Interpro	InterPro is an integrated database of predictive protein "signatures" used for the classification and automatic annotation of proteins and genomes	Database : Protein Signatures	Web		June 24, 2010	Home Page
Uniprot	comprehensive, high-quality and freely accessible resource of protein sequence and functional information	Database : Protein Annotation	Web		June 24, 2010	Home Page
HPRD	The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome	Tool : Protein Interaction	Web		June 24, 2010	Home Page
MINT	Welcome to MINT, the Molecular INTeraction database. MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators	Tool : Protein Interaction	Web		June 24, 2010	Home Page
DIP	The DIPTM database catalogs experimentally determined interactions between protein	Tool : Protein Interaction	Web		June 24, 2010	Home Page
Relibase	Easy searching of protein-ligand complexes	Tool : Sequence Analysis	Web		June 24, 2010	Home Page
MIPS PPI	The MIPS Mammalian Protein-Protein Interaction Database is a collection of manually curated high-quality PPI data collected from the scientific literature by expert curators	Database : Interaction	Web		June 24, 2010	Home Page
IntAct	IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.	Database : Interaction	Web		June 24, 2010	Home Page
BMM Domain Fishing	This server looks for recognizable protein domains in your amino acid sequence.	Tool : Sequence Analysis	Web		June 24, 2010	Home Page
Human Protein Atlas	The human protein atlas shows expression and localization of proteins in a large variety of normal human tissues, cancer cells and cell lines with the aid of immunohistochemistry (IHC) images and immunofluorescence (IF) confocal microscopy images.	Database : Protein Annotation	Web		June 24, 2010	Home Page
WormPep	Wormpep contains the predicted proteins from the Caenorhabditis elegans genome sequencing project.	Database : Protein Annotation	Web		June 24, 2010	Home Page
HUGE	A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project	Database : Protein Annotation	Web		June 24, 2010	Home Page
PMD	The Protein Mutant Database (PMD) that we are constructing covers natural as well as artificial mutants, including random and site-directed ones, for all proteins except members of the globin and immunoglobulin f	Database : Protein Annotation	Web		June 24, 2010	Home Page
Smart	SMART (Simple Modular Architecture Research Tool) is a web tool for the identification and annotation of protein domains	Database : Protein Annotation	Web		June 24, 2010	Home Page
ProtoNet	ProtoNet: Automatic hierarchical classifications of proteins	Database : Protein Annotation	Web		June 24, 2010	Home Page
PIRSF	The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships	Database : Protein Annotation	Web		June 24, 2010	Home Page
SUPERFAMILY	SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.	Database : Protein Annotation	Web		June 24, 2010	Home Page
Uniprot	The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.	Database : Protein Annotation	Web		June 24, 2010	Home Page
EPD	The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters	Database : Gene Regulation	Web		June 24, 2010	Home Page
CODHOP	PCR primers designed from protein multiple sequence alignments	Tool : Molecular Biology	Web		June 24, 2010	Home Page
Primer3	Pick primers from a DNA sequence	Tool : Molecular Biology	Web, Download		June 24, 2010	Home Page
AmplifX	The main purpose of AmplifX is to search through a collection of primers	Tool : Molecular Biology	Windows, Mac		June 24, 2010	Home Page
PrimerZ	PrimerZ: streamlined primer design for promoters, exons and human SNPs	Tool : Molecular Biology	Web		June 24, 2010	Home Page
SNPBox	SNPbox is a modular software package that automates the design of PCR primers for large-scale amplification and sequencing projects	Tool : Molecular Biology	Web		June 24, 2010	Home Page
PerlPrimer	PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR.	Tool : Molecular Biology	Web		June 24, 2010	Home Page
PASSML	A computer program called PASSML ('Phylogeny and Secondary Structure using Maximum Likelihood') has been developed to implement an evolutionary model that combines protein secondary structure and amino acid replacement	Tool : Sequence Analysis : Phylogeny	Source		June 24, 2010	Home Page
PHYLIP	PHYLIP is a free package of programs for inferring phylogenies	Tool : Sequence Analysis : Phylogeny	Windows, Mac, Linux, Source		June 24, 2010	Home Page
MOLPHY	MOLPHY: A Computer Program Package for Molecular Phylogenetics	Tool : Sequence Analysis : Phylogeny	UNIX, Source		June 24, 2010	Home Page
PAML 4	PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Tool : Sequence Analysis : Phylogeny	Windows, Mac, Linux		June 24, 2010	Home Page
PAUP *4.0	Software package for inference of evolutionary trees	Tool : Sequence Analysis : Phylogeny	Windows, Mac, UNIX, VMS		June 24, 2010	Home Page
Phase	PHASE is a package that performs molecular phylogenetic inference. The software seeks to accurately compare molecular sequences to determine the likely evolutionary relationships between a group of species	Tool : Sequence Analysis : Phylogeny	Windows, Linux, Source		June 24, 2010	Home Page
Beast	BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree	Tool : Sequence Analysis : Phylogeny	Windows, Mac, UNIX, Source		June 24, 2010	Home Page
Mac5	MAC5 implements MCMC sampling of the posterior distribution of tree topologies from DNA sequences containing gaps by using a five state model of evolution (the four nucleotides and the gap character)	Tool : Sequence Analysis : Phylogeny	Windows, Mac, UNIX, Source		June 24, 2010	Home Page
PhyloPat	Phylogenetic patterns show the presence or absence of certain genes or proteins in a set of sp	Tool : Sequence Analysis : Phylogeny	Web		June 24, 2010	Home Page
MrBayes	MrBayes is a program for the Bayesian estimation of phylogeny	Tool : Sequence Analysis : Phylogeny	Web		June 24, 2010	Home Page
FigTree	FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures	Tool : Sequence Analysis : Phylogeny	Java		June 24, 2010	Home Page
TreeBase	TreeBASE is a relational database of phylogenetic information	Tool : Sequence Analysis : Phylogeny	Web		June 24, 2010	Home Page
BAMBE	Bayesian Analysis in Molecular Biology and Evolution (BAMBE) is a free software package for the Bayesian analysis of phylogenies	Tool : Sequence Analysis : Phylogeny	Windows, UNIX		June 24, 2010	Home Page
JCVI Primer Designer	High throughput PCR primer design software.	Tool : Molecular Biology			June 24, 2010	Home Page
KEGG	KEGG: Kyoto Encyclopedia of Genes and Genomes	Database : Network Analysis : Pathway	Web		June 24, 2010	Home Page
Genstruct	Genstruct: automating and optimizing the pharmaceutical drug development process.	Tool : Network Analysis : Pathway	Web, Commercial		June 24, 2010	Home Page
Ingenuity	Technologies that help life science researchers more effectively search, explore, visualize, and analyze biological and chemical findings related to genes, proteins, and small molecules (e.g. drugs)	Database : Tool : Network Analysis : Pathway	Web, Commercial		June 24, 2010	Home Page
KEGG	Pathway maps	Database : Network Analysis : Pathway	Web		June 24, 2010	Home Page
Exonerate	Exonerate is a generic tool for pairwise sequence comparison	Tool : Sequence Analysis	Web		June 24, 2010	Home Page
HCOP	HGNC Comparison of Orthology Predictions	Tool : Sequence Analysis	Web		June 24, 2010	Home Page
MitoDat	MitoDat - Mendelian Inheritance and the Mitochondrion	Database : Organelle	Web		June 24, 2010	Home Page
GOBASE	GOBASE is a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts	Database : Organelle	Web		June 24, 2010	Home Page
CTD	The Comparative Toxicogenomics Database (CTD) elucidates molecular mechanisms by which environmental chemicals affect human disease	Database : Ontology	Web		June 24, 2010	Home Page
PeroxisomeDB	PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome	Database : Organelle	Web		June 24, 2010	Home Page
Ontology Evolution Explorer (OnEX)	The Ontology Evolution Explorer (OnEX) is a web-based system for exploring ontology changes.	Tool : Ontology	Web		June 24, 2010	Home Page
COBrA	Browse and search and edit GO and OBO formatted ontology information	Tool : Ontology	Java		June 24, 2010	Home Page
BioMagResBank	A repository for Data from NMR Spectroscopy on Proteins, Peptides and Nucleic Acids	Database : Proteomics	Web		June 24, 2010	Home Page
LNA tools	LNA (Locked Nucleic Acid) melting temperature prediction tool	Tool : Molecular Biology	Web		June 24, 2010	Home Page
Expression Profiler	Expression Profiler: An open extensible web-based collaborative platform for microarray gene expression, protein protein interaction and next gen sequence	Tool : Gene Expression : Microarray : Next-Generation Sequencing	Web		June 24, 2010	Home Page
CLC Workbench	CLC Genomics Workbench, for analyzing and visualizing Next Generation Sequencing data, incorporates cutting-edge technology and algorithms	Tool : Next-Generation Sequencing	Web, Commercial		June 24, 2010	Home Page
ERANGE	ERANGE is a Python package for doing RNA-seq and ChIP-seq	Tool : Next-Generation Sequencing	Mac, Linux, Python		June 24, 2010	Home Page
SISSRS	SISSRs (Site Identification from Short Sequence Reads), a novel algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments	Tool : Next-Generation Sequencing	Perl		June 24, 2010	Home Page
Wold Lab Software Suite	The Wold Bioinformatics Lab Software Suite	Tool : Next-Generation Sequencing	Python		June 24, 2010	Home Page
QuEST	QuEST is a Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitations (ChIP-Seq or ChIPseq).	Tool : Next-Generation Sequencing	Source		June 24, 2010	Home Page
ChIPDiff	Genome-wide Identification of Differential Histone Modification Sites from ChIP-Seq Data". Bioinformatics, 24:2344-2349	Tool : Next-Generation Sequencing	Source		June 24, 2010	Home Page
FindPeaks	FindPeaks: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology	Tool : Next-Generation Sequencing	Java		June 24, 2010	Home Page
Biolayout Express	BioLayout Express3D is a tool for the visualization and analysis of networks derived from biological systems	Tool : Network Analysis	Windows, Mac, Linux, Source		June 24, 2010	Home Page
PBMice	PBmice provides integrated information of PiggyBac insertional mutations and their characterizations in mice	Database : Gene Mutant	Web		June 24, 2010	Home Page
chipSeq Peak Finder	The ChIP-Seq peak finder version 2.0 and higher is actually now part of the ERANGE package	Tool : Next-Generation Sequencing	Mac, Linux, Python		June 24, 2010	Home Page
JDesigner2	A graphical editor for network models described by biochemical reactions such as signalling, metabolic or gene regulatory networks.	Tool : Network Analysis	Windows, Mac, Linux		June 24, 2010	Home Page
Clustal	Multiple alignment of nucleic acid and protein sequences	Tool : Sequence Analysis	Web, Download		June 24, 2010	Home Page
Se-Al	Se-Al is an application for creating multiple sequence alignments from nucleotide and amino acid sequences	Tool : Sequence Analysis	Mac		June 24, 2010	Home Page
M-coffee	Meta multiple sequence alignment	Tool : Sequence Analysis	Web		June 24, 2010	Home Page
T-coffee	T-coffee is a multiple sequence alignment tool	Tool : Sequence Analysis	Web		June 24, 2010	Home Page
CoMoDis	Composite Motif Discovery (CoMoDis), which streamlines computational identification of novel regulatory modules	Tool : Gene Regulation			June 24, 2010	Home Page
EMMA	EMMA--mouse mutant resources for the international scientific community	Database : Gene Mutant	Web		June 24, 2010	Home Page
Molecular Interation Maps	A Molecular Interaction Map (MIM) is a diagram convention that is capable of unambiguous representation of networks containing multi-protein complexes, protein modifications, and enzymes that are substrates of other enzymes	Tool : Interaction	Web		June 24, 2010	Home Page
Cytoscape	Platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data.	Tool : Interaction	Windows, Mac, Linux, UNIX		June 24, 2010	Home Page
REBASE	The Restriction Enzyme Database	Tool : Molecular Biology	Web		June 24, 2010	Home Page
pDRAW	pDRAW32 DNA analysis software	Tool : Molecular Biology	Windows, Mac, Linux		June 24, 2010	Home Page
MapMi	MapMi is a tool designed to locate miRNA precursor sequences in existing genomic sequences	Tool : RNA	Web		June 24, 2010	Home Page
VectorDB	VectorDB contains annotations and sequence information for many vectors commonly used in molecular biology	Tool : Molecular Biology	Web		June 24, 2010	Home Page
Doelan	A monitoring tool for quality of spotted arrays	Tool : Microarray	Java		June 24, 2010	Home Page
TM4	Microarray Gene Expression suite including image analysis, database,spotfinding and data conversion	Tool : Microarray	Windows, Mac, Linux, UNIX		June 24, 2010	Home Page
ProbeLynx	ProbeLynx offers microarray users the ability to upload their probe sequences and continuously assess probe specificity and annotation based on latest releases of genomic sequence data and gene prediction	Tool : Microarray	Web		June 24, 2010	Home Page
DEEP	Deep takes differential gene expression data and predicts additional molecules which may be important in either of the two tissues under examination by integrating information on signaling stored in the TRANSPATH database	Tool : Functional Analysis	Web		June 24, 2010	Home Page
Cluster and TreeView	A system of cluster analysis for genome-wide expression data from DNA microarray hybridization that arranges genes according to similarity in pattern of gene expression.	Tool : Microarray	Windows		June 24, 2010	Home Page
TiGR Spotfinder	Microarray Image Analysis Suite	Tool : Microarray	Windows, Mac, Linux, UNIX		June 24, 2010	Home Page
ScanAlyze	Process fluorescent images of microarrays. Includes semi-automatic definition of grids and complex pixel and spot analyses	Tool : Microarray	Windows		June 24, 2010	Home Page
MADAM: MicroArray DAta Manager	MADAM facilites the entry of data into a microarray database	Database : Microarray	Windows, Mac, Linux, UNIX		June 24, 2010	Home Page
ArrayExpress	ArrayExpress microarray database and gene expression Atlas tool	Database : Gene Expression : Microarray	Web		June 24, 2010	Home Page
caArray	Array Data Management System: open-source, web and programmatically accessible array data management system.	Database : Gene Expression : Microarray : Disease : Cancer	Web		June 24, 2010	Home Page
StemBase	StemBase is a database of gene expression data obtained from stem cells and derivatives mainly from mouse and human using DNA microarrays and Serial Analysis of Gene Expression	Database : Gene Expression : Microarray	Web		June 24, 2010	Home Page
BASE	BASE is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis.	Database : Gene Expression : Microarray	Windows, Mac, Linux		June 24, 2010	Home Page
MAGE	The purpose of the MicroArray Gene Expression (MAGE) project is to unify all of the most popular microarray storage/usage formats into a single standard that will eventually be used by all. MAGE will replace MAML, GEML, GeneXML, et al.	Database : Gene Expression : Microarray			June 24, 2010	Home Page
SMD	The Stanford Microarray Database serves as a microarray research database for Stanford investigators and their collaborators	Database : Gene Expression : Microarray	Web		June 24, 2010	Home Page
MIAMExpress	Data submission tool to the Array Express Database	Tool : Gene Expression : Microarray	Web		June 24, 2010	Home Page
CIBEX	CIBEX is a public database for microarray data, which is aimed at storing MIAME-compliant data in accordance with MGED Society recommendations.	Database : Gene Expression : Microarray	Web		June 24, 2010	Home Page
HOOK	Calibration of data from Affymetrix Oligonucleotide Arrays based on a model motivated by the specific chemical and physical properties of these arrays	Tool : Gene Expression : Microarray	Java		June 24, 2010	Home Page
Express Yourself	Microarray Data Processing Platform	Tool : Gene Expression : Microarray	Web		June 24, 2010	Home Page
simpleaffy	Purpose: High level functions for working with data from Affymetrix Oligonucleotide Arrays	Tool : Gene Expression : Microarray	Windows, Mac, UNIX		June 24, 2010	Home Page
flexclust	Purpose: Implementations of common clustering algorithms, e.g. k-centroids and QT clustering	Tool : Gene Expression : Microarray	Windows, Mac, UNIX		June 24, 2010	Home Page
genefilter	Purpose: Provides basic gene filtering functions	Tool : Gene Expression : Microarray	Windows, Mac, UNIX		June 24, 2010	Home Page
ggplot2	Purpose: Advanced visualization package, providing sophisticated graphic functions to prepare suitable images for publications	Tool : Gene Expression : Microarray	Windows, Mac, UNIX		June 24, 2010	Home Page
limma	Purpose: Data analysis for Microarray data, e.g. differential expression discovery and calculation of linear models	Tool : Gene Expression : Microarray	Windows, Mac, UNIX		June 24, 2010	Home Page
pamr	Purpose: prediction analysis for microarrays	Tool : Gene Expression : Microarray	Windows, Mac, UNIX		June 24, 2010	Home Page
samr	Purpose: Significance Analysis of Microarrays	Tool : Gene Expression : Microarray	Windows, Mac, UNIX		June 24, 2010	Home Page
Agi4x44PreProcess	Purpose: Preprocessing of Agilent 4x44 array data	Tool : Gene Expression : Microarray	Windows, Mac, UNIX		June 24, 2010	Home Page
affy	Purpose: Reads Affymetrix Oligonucleotide Arrays	Tool : Gene Expression : Microarray	Windows, Mac, UNIX		June 24, 2010	Home Page
lumi	Purpose: Reads Illumina BeadArray microarray data	Tool : Gene Expression : Microarray	Windows, Mac, UNIX		June 24, 2010	Home Page
CAT-Score	Purpose: Correlation-Adjusted t Score	Tool : Gene Expression : Microarray	Windows, Mac, UNIX		June 24, 2010	Home Page
INCLUSive	INCLUSive is a suite of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements	Tool : Gene Regulation : Sequence Analysis	Web		June 24, 2010	Home Page
CARMAweb	R-based web service for microarray analysis	Tool : Gene Expression : Microarray	Web		June 24, 2010	Home Page
GENESET	Provides variable selection for high-dimensional data, e.g. that obtained in gene expression experiments. The method constructs sets of significantly related variables.	Tool : Gene Expression : Microarray			June 24, 2010	Home Page
ProdoNet	ProdoNet is a visualisation tool for regulatory networks from the PRODORIC bacterial database. It detects common regulators and metabolic pathways from a list of genes or proteins.	Tool : Metabolomics	Web		June 24, 2010	Home Page
Monosccharide Browser	The monosaccharide browser allows you to view space filling Fischer projections of monosaccharides	Tool : Metabolomics	Web		June 24, 2010	Home Page
IMPACT	IMPACT is a 3 year, EU-funded project to continue to develop and enhance InterPro and it's contributing databases (Gene3D, Pfam, PRINTS, ProDom, Prosite, SMART, SuperFamily).	Tool : Sequence Analysis	Web		June 24, 2010	Home Page
PathExpress	PathExpress is a web-based tool developed to interpret gene expression data obtained from microarray experiments by identifying the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes).	Tool : Metabolomics	Web		June 24, 2010	Home Page
METANNOGEN	METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks	Tool : Metabolomics : Network	Web		June 24, 2010	Home Page
OligoWiz 2	Intelligent design of oligonucleotides for DNA microarrays	Tool : Molecular Biology	Java		June 24, 2010	Home Page
MASCOT	This site features Mascot, a powerful search engine that uses mass spectrometry data to identify proteins from primary sequence databases	Tool : Proteomics	Web, Commercial		June 24, 2010	Home Page
InSilicoArray CGH	Merging DNA copy number and expression chromosomal clustering	Database : Chromosomal : Gene Expression : Integrated Analysis	Web		June 24, 2010	Home Page
OligoArray 2	Genome scale oligonucleotide design	Tool : Molecular Biology	Web		June 24, 2010	Home Page
Martini	Martini uses literature keywords to compare gene sets	Tool : Literature Mining	Web		June 24, 2010	Home Page
Manatee	Manatee is a web-based tool used to perform manual functional annotation.	Tool : Gene Annotation	Web		June 24, 2010	Home Page
CoPub	CoPub is a text mining tool that detects co-occuring biomedical concepts in abstracts from the MedLine literature database.	Tool : Literature Mining	Web		June 24, 2010	Home Page
BioGPS	A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function	Database : Gene Expression : Integrated Analysis	Web		June 24, 2010	Home Page
BIOBASE	BIOBASE Knowledge Library	Information	Commercial		June 24, 2010	Home Page
Amazonia	A free web atlas that allows an easy query of public human transcriptome data by keyword in thematic pages and with list annotation	Database : Gene Expression : Integrated Analysis	Web		June 24, 2010	Home Page
IntegromeDB	IntegromeDB, a semantic graph-based ‘deep-web’ data integration system that automatically captures, integrates and manages publicly available data concerning transcriptional regulation	Database : Integrated Analysis	Windows, Mac		June 24, 2010	Home Page
Genevestigator	Genevestigator is a high quality and manually curated expression database and meta-analysis system	Tool : Integrated Analysis	Java, Commercial		June 24, 2010	Home Page
Inforsense	The InforSense platform is a next generation BI solution that enables organizations to quickly create analytical applications based on any data source in any format, however complex	Tool : Integrated Analysis	Commercial		June 24, 2010	Home Page
Partek Genomics Suite	Partek Genomics Suite provides innovative solutions for integrated genomics and is unique in supporting all microarray and next generation sequencing technologies including DGE and gene expression, RNA-seq and alternative splicing, copy number and association, ChIP-chip, ChIP-seq, and microRNA	Tool : Integrated Analysis	Commercial		June 24, 2010	Home Page
Spotfire	Improved Decision-making across the Enterprise	Tool : Integrated Analysis			June 24, 2010	Home Page
TFBSCluster	This web tool is designed to identify clusters of transcription factor binding sites (TFBSs) that are conserved between mammalian genomes	Tool : Gene Regulation : Sequence Analysis	Web		June 24, 2010	Home Page
FlyView	A Drosophila Image Database	Database : Image	Web		June 24, 2010	Home Page
SWISS-3DIMAGE	SWISS-3DIMAGE is an image database which strives to provide high quality pictures of biological macromolecules with known three-dimensional structure	Database : Image	Web		June 24, 2010	Home Page
PaLS	Pals filters sets of lists for gene identifiers	Tool : Gene Annotation	Web		June 24, 2010	Home Page
BioImage Suite	BioImage Suite is an integrated image analysis software suite developed	Tool : Image	Windows, Mac, Linux		June 24, 2010	Home Page
Clone/Gene ID Mapping	To help researchers map accession numbers and identifiers among clones, genes, proteins and chromosomal positions, we have designed and developed IDconverter and IDClight.	Tool : Gene Annotation	Web		June 24, 2010	Home Page
GoFish	GoFish allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes	Tool : GO	Java, Source		June 24, 2010	Home Page
GenNav	Gene Ontology search and visualisation tool	Tool : GO	Web		June 24, 2010	Home Page
GONUT	The GONUTS wiki has been set up to provide third-party documentation for users of the Gene Ontology Project	Database : GO	Web		June 24, 2010	Home Page
OBO-Edit	Browse and search OBO formatted ontology information	Tool : GO	Java		June 24, 2010
Amigo	Browse and search the ontology information provided by the GO consortium	Tool : GO	Java		June 24, 2010	Home Page
GOEAST	GO analysis of Gene Ontology within Microarray Gene Expression Experiments	Tool : GO : Functional Analysis	Web		June 24, 2010	Home Page
GoSurfer	GoSurfer is an easy-to-use graphical exploration tool with built-in statistical features that allow a rapid assessment of the biological functions.	Tool : GO : Functional Analysis	Windows		June 24, 2010	Home Page
GoEast	GOEAST is web based software toolkit providing easy to use, visualizable, comprehensive and unbiased Gene Ontology (GO) analysis for high-throughput experimental results	Tool : GO : Functional Analysis	Web		June 24, 2010	Home Page
DynGO	DynGO: A Tool for Browsing and Mining Gene Ontology and Its Associations	Tool : GO	Perl, Java		June 24, 2010	Home Page
OLS	The Ontology Lookup Service is a spin-off of the PRIDE project, which required a centralized query interface for ontology and controlled vocabulary lookup	Tool : GO	Web		June 24, 2010	Home Page
MGI GO Browser	MGI GO Browser	Tool : GO	Web		June 24, 2010	Home Page
ALFRED	Allele Frequency Database: A resource of gene frequency data in human populations	Database : Genome	Web		June 24, 2010	Home Page
EGA	The European Genome-phenome Archive (EGA) is designed to be a repository for all types of genotype experiments, including case control, population, and family studies	Database : Genome	Web		June 24, 2010	Home Page
CGAP GO Browser	Browse the GO Ontology	Tool : GO	Web		June 24, 2010	Home Page
MGI GO Browser	Browse the GO Ontology at the MGI	Tool : GO	Web		June 24, 2010	Home Page
IMGT	An integrated knowledge resource specialized in the immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF), major histocompatibility complex superfamily (MhcSF) and related proteins of the immune system (RPI)	Database : Genome	Web		June 24, 2010	Home Page
Asterias	Suite of genomic and proteomic analysis tools	Tool : Genome	Web		June 24, 2010	Home Page
Progenetix CGH database	Progenetix - Genomic Profiling in Cancer	Database : Genome Annotation : Gene Expression Analysis	Web		June 24, 2010	Home Page
1000 Genomes	A Deep Catalog of Human Genetic Variation	Database : Genome	Web		June 24, 2010	Home Page
GMOD	GMOD is the Generic Model Organism Database project, a collection of open source software tools for creating and managing genome-scale biological databases	Tool : Genome			June 24, 2010	Home Page
GPAT	Retrieve annotation from mouse and human genomic positions	Tool : Genome	Web		June 24, 2010	Home Page
Xenbase	Xenbase: Xenopus laevis and Xenopus tropicalis biology and genomics resource	Database : Genome	Web		June 24, 2010	Home Page
Flybase	Drosophila genome database	Database : Genome Annotation	Web		June 24, 2010	Home Page
Entrez Genome	Entrez Genome database provides views for a variety of genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps.	Database : Genome	Web		June 24, 2010	Home Page
VisGenome	VisGenome: visualization of single and comparative genome representations	Tool : Genome	Web		June 24, 2010	Home Page
Array Studio	Array Studio is a software package which provides state of the art statistics and visualization for the analysis of high dimensional quantification data	Tool : Gene Expression : Microarray	Windows, Commercial		June 24, 2010	Home Page
Gbrowse	The Generic Genome Browser (GBrowse) is a combination of database and interactive Web page for manipulating and displaying annotations on genomes	Tool : Genome	Web		June 24, 2010	Home Page
GenomeGraphs	Plotting genomic information from Ensembl	Tool : Genome	Web		June 24, 2010	Home Page
ZFIN	The Zebrafish Model Organism Database	Database : Genome Annotation	Web		June 24, 2010	Home Page
MEPD	This database contains Medaka gene expression data examined through whole mount in situ hybridization	Database : Genome Annotation	Web		June 24, 2010	Home Page
ArkDB	The ArkDB database system aims to provide a comprehensive public repository for genome mapping data from farmed and other animal Species	Database : Genome Annotation	Web		June 24, 2010	Home Page
Fugu Genome Project	The fugu (Takifugu rubripes or Fugu rubripes) genome project database	Database : Genome Annotation			June 24, 2010	Home Page
RatMap	The Rat Genome Database RatMap is focused on presenting rat genes, DNA-markers, QTL:s etc that is localized to chromosome	Database : Genome Annotation	Web		June 24, 2010	Home Page
BOVMAP	Mapping the Bovine Genome	Database : Genome Annotation	Web		June 24, 2010	Home Page
OMIA	Online Mendelian Inheritance in Animals (OMIA) is a database of genes, inherited disorders and traits in more than 135 animal species	Database : Genome Annotation	Web		June 24, 2010	Home Page
DagClainer	Computing chains of syntenic genes in complete genomes	Tool : Genomic Annotation	Java		June 24, 2010	Home Page
Jbrowse	Open source, portable, JavaScript-based genome browser	Database : Genome Annotation	Web		June 24, 2010	Home Page
BioSapiens	BioSapiens is a Network of Excellence, funded by the European Union's 6th Framework Programme, and made up of bioinformatics researchers from 25 institutions based in 14 countries throughout Europe	Database : Genome Annotation	Web		June 24, 2010	Home Page
DictyBase	Dictyostelid genomics	Database : Genome Annotation	Web		June 24, 2010	Home Page
EnsMart	EnsMart: a generic system for fast and flexible access to biological data	Database : Genome Annotation	Web		June 24, 2010	Home Page
Entrez Genome	The Genome database provides views for a variety of genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps	Database : Genome Annotation	Web		June 24, 2010	Home Page
BDGP	Berkeley Drosophila Genome Project	Database : Genome Annotation	Web		June 24, 2010	Home Page
MGI	Mouse Genome Informatics Database	Database : Genome Annotation	Web		June 24, 2010	Home Page
SGD	Saccharomyces genome database	Database : Genome Annotation	Web		June 24, 2010	Home Page
Wormbase	The biology and genome of C.elegans	Database : Genome Annotation	Web		June 24, 2010	Home Page
RGD	Rat Genome Database	Database : Genome Annotation	Web		June 24, 2010	Home Page
PASA	PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool	Database : Genome Annotation	Linux, UNIX		June 24, 2010	Home Page
SpliceCenter	SpliceCenter is a suite of user-friendly tools that evaluate the impact of gene splicing variation on specific molecular biology techniques	Tool : Gene Annotation	Web		June 24, 2010	Home Page
Mummer	MUMmer is a system for rapidly aligning entire genomes	Tool : Genome	UNIX		June 24, 2010	Home Page
SpliceMiner	Human splice variants	Tool : Gene Annotation	Web		June 24, 2010	Home Page
Biotapestry	Tool for building and visualising gene regulatory networks	Tool : Gene Regulation	Windows, Mac, Linux, UNIX, Source		June 24, 2010	Home Page
JIGSAW	JIGSAW: integration of multiple sources of evidence for gene prediction	Tool : Gene Prediction	Web		June 24, 2010	Home Page
Genomatix Software	Understanding gene regulation	Tool : Gene Regulation	Web, Commercial		June 24, 2010	Home Page
ENCODE	Encyclopedia Of DNA Elements- a project to identify all functional elements in the human genome sequence	Tool : Gene Regulation			June 24, 2010	Home Page
GFINDer	A tool to support the annotation of gene lists	Tool : Gene Annotation	Web		June 24, 2010	Home Page
CGAP GO Browser	Cancer Genome Anatomy Project Gene Ontology Browser	Tool : GO	Web		June 24, 2010	Home Page
MILANO	This program performs automatic searches in PubMed or the GeneRIF collection for articles containing co-occurrences of search terms with a list of genes (e.g. from a microarray experiment)	Tool : Gene Annotation	Web		June 24, 2010	Home Page
Dragon	The (Dragon) annotate tool allows you to append multiple types of biological information to large lists of genes	Tool : Gene Annotation	Web		June 24, 2010	Home Page
MatchMiner	MatchMiner is a set of tools that enables the user to translate between disparate ids for the same gene	Tool : Gene Annotation	Web		June 24, 2010	Home Page
MAPPFinder	Using Gene Ontology and Genmapp for functional analysis of gene expression data	Tool : Gene Expression : GO : Functional Analysis	Windows		June 24, 2010	Home Page
PathwayExplorer	A web service for visualising gene expression data on biological pathways	Tool : Gene Expression : Functional Analysis	Web		June 24, 2010	Home Page
GEDI	Visualization of gene expression data using self organizing maps	Tool : Gene Expression	Java		June 24, 2010	Home Page
GenMapp	GenMapp: viewing and analysis of gene expression data on pathways	Tool : Gene Expression : GO : Pathway	Windows		June 24, 2010	Home Page
BTW	Boltzmann timewarping can be used to compare different time series gene expression datasets	Tool : Gene Expression	Web		June 24, 2010	Home Page
SMD	Stanford Microarray Database	Database : Gene Expression	Web		June 24, 2010	Home Page
RAD	RAD is a resource for gene expression studies, which stores highly curated MIAME-compliant studies (i.e. experiments) employing a variety of technologies such as filter arrays, 2-channel microarrays, Affymetrix chips, SAGE, MPSS and RT-PCR	Database : Gene Expression	Web		June 24, 2010	Home Page
geneX	An open source gene expression database	Database : Gene Expression	Perl		June 24, 2010	Home Page
SIB-CleanEx	CleanEx is a database which provides access to public gene expression data via unique approved gene symbols and which represents heterogeneous expression data.	Database : Gene Expression	Web		June 24, 2010	Home Page
ExpressDb	ExpressDB was originally a relational database containing yeast and E. coli RNA expression data.	Database : Gene Expression	Web		June 24, 2010	Home Page
4DXpress	This database provides a platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse).	Tool : Gene Expression	Web		June 24, 2010	Home Page
Bgee	Bgee: a dataBase for Gene Expression Evolution	Tool : Gene Expression	Web		June 24, 2010	Home Page
smiRNAdb	smiRNAdb is a database containing expression information for human, mouse, rat, zebrafish, worm and fruitfly small RNAs (mostly miRNAs).	Database : Gene Expression : RNA	Web		June 24, 2010	Home Page
GEMS	Gene Expression Module Sampler a gene expression biclustering tool	Tool : Gene Expression	Web		June 24, 2010	Home Page
MAGMA	Two colour gene expression analysis	Tool : Gene Expression : Microarray	Web		June 24, 2010	Home Page
CIMminer	CIMminer generates color-coded Clustered Image Maps to represent "high-dimensional" data sets such as gene expression profiles.	Tool : Gene Expression	Web, Java		June 24, 2010	Home Page
MADNet	MADNet is an analysis and visualization tool for microarray data mining. Genes from a single gene or microarray experiment are designated on the maps of known metabolic and signaling pathways together with transcription factors and drug targets.	Tool : Gene Expression : Microarray	Web		June 24, 2010	Home Page
GeWare	The Genetic Data Warehouse allows you to load, analyse and store Gene Expression and Matrix-CGH (Array CGH) data	Database : Tool : aCGH : Gene Expression : Microarray	Web		June 24, 2010	Home Page
POXO	POXO is a series of tools that can be used to discover, search and verify possible regulatory cis-element(s) from set(s) co-expressed genes.	Tool : Gene Expression : Gene Regulation	Web		June 24, 2010	Home Page
GEMLeR	GEMLeR provides a collection of gene expression datasets that can be used for benchmarking gene expression oriented machine learning algorithms.	Tool : Gene Expression	Web		June 24, 2010	Home Page
GEPS	Gene Expression Pattern Scanner	Tool : Gene Expression	Web		June 24, 2010	Home Page
Gepas	A web-based pipeline for microarray gene expression profile analysis	Tool : Gene Expression	Web		June 24, 2010	Home Page
GenePublisher	GenePublisher performs automated data analysis from gene expression experiments on a number of different platforms	Tool : Gene Expression	Web		June 24, 2010	Home Page
VAMPIRE	VAMPIRE is a collection of Java tools designed to perform Bayesian statistical analysis of gene expression array data.	Tool : Gene Expression : Microarray	Java		June 24, 2010	Home Page
TIGER	TiGER is a database developed by the Bioinformatics Lab at Wilmer Eye Institute of Johns Hopkins University. The database contains tissue-specific gene expression profiles or expressed sequence tag (EST) data, cis-regulatory module (CRM) data, and combinatorial gene regulation data.	Database : Gene Annotation	Web		June 24, 2010	Home Page
Genespring GX	GeneSpring GX provides powerful, accessible statistical tools for fast visualization and analysis of expression and genomic structural variation data	Tool : aCGH : Gene Expression : Microarray	Windows, Mac, Linux, Commercial		June 24, 2010	Home Page
OMIM	OMIM, Online Mendelian Inheritance in Man, a database of human genes and genetic disorders	Database : Gene Annotation	Web		June 24, 2010	Home Page
BioGPS	A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function	Database : Protein Annotation : Gene Annotation			June 24, 2010	Home Page
HOVERGEN	HOVERGEN is a database of homologous vertebrate genes.	Database : Gene Annotation	Web		June 24, 2010	Home Page
BioGPS	A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function.	Database : Gene Annotation	Web		June 24, 2010	Home Page
WorfDB	The C. elegans ORFeome cloning projec	Database : Gene Annotation	Web		June 24, 2010	Home Page
GENCODE	The aim of GENCODE as a sub-project of the ENCODE scale-up project is to annotate all evidence-based gene features in the entire human genome at a high accuracy	Database : Gene Annotation	Web		June 24, 2010	Home Page
GermOnline	The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction	Database : Gene Annotation	Web		June 24, 2010	Home Page
The gene index project (TGI)	The goal of The Gene Index Project is to use the available EST and gene sequences, along with the reference genomes wherever available, to provide an inventory of likely genes and their variants and to annotate these.	Database : Gene Annotation	Web		June 24, 2010	Home Page
GoMiner	Biological interpretation of gene lists in the context of the Gene Ontology	Tool : GO : Functional Analysis	Web, Java		June 24, 2010	Home Page
GENEATLAS	GENATLAS contains relevant information with respect to gene mapping and genetic diseases.	Database : Gene Annotation	Web		June 24, 2010	Home Page
g:profiler	g:Profiler (http://biit.cs.ut.ee/gprofiler/) is a public web server for characterising and manipulating gene lists resulting from mining high-throughput genomic data.	Tool : Functional Analysis	Web		June 24, 2010	Home Page
Babelomics	Functional set enrichment and annotation package	Tool : Functional Analysis	Web		June 24, 2010	Home Page
FUGE	FuGE is a model of the shared components in different functional genomics domains.	Information : Data Format			June 24, 2010	Home Page
PANTHER		Database : Tool : Functional Analysis : SNP	Web		June 24, 2010	Home Page
Onto-Tools	A suite of tools for functional analysis of genomic data	Database : Tool : Functional Analysis : SNP	Web		June 24, 2010	Home Page
GeneTrail	The statistical evaluation of high-throughput genomic or proteomic data sets with respect to enrichment of functional categories	Tool : Functional Analysis	Web		June 24, 2010	Home Page
GeneSigDB	Curated gene expression signature database	Tool : Integrated Analysis	Web		June 24, 2010	Home Page
Caryoscope	Caryoscope: a tool for visualizing microarray data from array comparative genome hybridization experiments in a genomic context	Chromosomal : Tool : Gene Expression	Web		June 24, 2010	Home Page
Systems Biology Markup Language (SBML)	SBML is an exchange format for computational models of biological processes, especially for the representation of phenomena at the scale of biochemical reactions.	Information : Data Exchange			June 24, 2010	Home Page
Pscan	Pscan is a software tool that scans a set of sequences from co-regulated or co-expressed genes with motifs describing the binding specificity of known transcription factors and assesses which motifs are significantly over- or under-represented	Tool : Gene Regulation : Sequence Analysis	Web		June 24, 2010	Home Page
kmer	Suite of tools for DNA sequence analysis - searching (EST, mRNA, sequencer reads); aligning (ESTs, mRNA, whole genome); and analysis (repeats, kmers).	Tool : Sequence Analysis	UNIX		June 24, 2010	Home Page
Tom	TOM: efficient identification of candidate genes responsible for multigenic diseases	Database : Disease	Web		June 24, 2010	Home Page
ZooDDD	ZooDDD: a cross-species database for digital differential display analysis.	Database : Gene Expression	Web		June 24, 2010	Home Page
SIMAP	SIMAP is a public database of pre-calculated protein similarities	Database : Proteins	Web		June 24, 2010	Home Page
DECIPHER	DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources	Database : Genomic Aberration	Web		June 24, 2010
BioVenn	BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams	Tool	Web		June 24, 2010	Home Page
MMIA	MMIA : microRNA and mRNA Integrated Analysis	Tool : Integrated Analysis : RNA	Web		June 24, 2010	Home Page
ELIXIR	The mission of ELIXIR is to construct and operate a sustainable infrastructure for biological information in Europe to support life science research and its translation to medicine and the environment, the bio-industries and society	Information : Infrastructure	Web		June 24, 2010	Home Page
EMBRACE	The objective of EMBRACE is to draw together a wide group of experts throughout Europe who are involved in the use of information technology in the biomolecular sciences	Information : Infrastructure	Web		June 24, 2010	Home Page
BiologicalNetworks	It integrates and visualises molecular interaction networks, metabolic and signaling pathways with experimental data, genomic sequences, 3D structure information, ontologies and taxonomies	Tool : Integrated Analysis	Windows, Mac		June 24, 2010	Home Page
Bioperl	A community effort to produce Perl code which is useful in biology	Tool	Perl		June 24, 2010	Home Page
Gnu Scientific Library	C++ library of algorithms for scientific computing, e.g. regarding differential equations, root finding, and least-squares fitting.	Tool	Mac, UNIX		June 24, 2010	Home Page
BioJava	BioJava is an open-source project dedicated to providing a Java framework for processing biological data	Tool	Java		June 24, 2010	Home Page
CRSD	The composite regulatory signature database can be applied in investigating complex regulatory behaviors involving the gene expression signatures , microRNA regulatory signatures and TF regulatory signatures .	Tool : Gene Regulation	Web		June 24, 2010	Home Page
Codon Usage Db	Codon Usage Database	Tool : Gene Regulation	Web		June 24, 2010	Home Page
VisHic	VisHiC is a public web server for clustering and interpreting gene expression data	Tool : Microarray	Web		June 24, 2010	Home Page
OSCAR	Cross species clustering tool	Tool : Microarray	Web		June 24, 2010	Home Page
POBO	POBO is a tool to summarize, verify and screen predetermined cis-elements from a set of sequences. POBO reports the results in as understandable format as possible for biologists.	Tool : Gene Regulation	Web		June 24, 2010	Home Page
GeneLoc	GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm.	Chromosomal : Tool	Web		June 24, 2010	Home Page
TICdb	TICdb: a collection of gene-mapped translocation breakpoints in cancer	Database : Tool : Disease : Cancer	Web		June 24, 2010	Home Page
FinchTV	A chromatogram viewer	Tool : Molecular Biology	Windows, Mac, Linux, UNIX		June 24, 2010	Home Page
4peaks	Application for viewing and editing sequence trace files	Tool : Molecular Biology	Windows, Mac		June 24, 2010	Home Page
Chromas Lite	Application for viewing and editing sequence trace files	Tool : Molecular Biology	Windows, Source		June 24, 2010	Home Page
Cancer Gene Census	The Cancer Gene Census is an ongoing effort to catalogue those genes for which mutations have been causally implicated in cancer.	Database : Disease : Cancer	Web		June 24, 2010	Home Page
caBIG	NCI caBig cancer informatics project	Database : Disease : Cancer	Web		June 24, 2010	Home Page
CMAP	Cancer molecular analysis project	Database : Tool : Disease : Cancer	Web		June 24, 2010	Home Page
CancerGenes	CancerGenes: a gene selection resource for cancer genome projects	Database : Disease : Cancer	Web		June 24, 2010	Home Page
caGEDA	A web application for the integrated analysis of global gene expression patterns in cancer	Database : Gene Expression : Integrated Analysis : Disease : Cancer	Web		June 24, 2010	Home Page
Goblet	Analysis of Blast sequence search hits in terms of GO annotation	Database : Ontology : GO	Web		June 24, 2010	Home Page
Bioportal	BioPortal to access and share ontologies that are actively used in biomedical communities.	Database : Ontology	Web		June 24, 2010	Home Page
Edinburgh Pathway Editor	EPE is a visual editor designed for annotation, visualisation and presentation of wide variety of biological networks, including metabolic, genetic and signal transduction pathways.	Tool : Network Analysis	Java		June 24, 2010	Home Page
Bifurcation Discovery Tool	Provides a genetic algorithm to search for Hopf bifurcations, turning points, and bistable switches.	Modelling : Bifurcation Analysis	Windows, Mac, Linux		June 24, 2010	Home Page
EBI	A major centre for bioinformatics, managing a large number of diverse resources and offering many publicly available bioinformatics services	Information : Bioinformatics Centre	Web		June 24, 2010	Home Page
MaRe	Batch retrieval of microarray data from GEO and Array Express Gene Expression Databases	Tool : Microarray	Web		June 24, 2010	Home Page
AbMiner	Search tool for commericially available antibodies	Database : Antibodies	Web		June 24, 2010	Home Page
KARMA	Array annotation and manager tool	Database : Microarray Annotation	Web		June 24, 2010	Home Page
ProServer	ProServer: a simple, extensible Perl DAS server	Database : Annotation	Perl		June 24, 2010	Home Page
FlyBrain	Online atlas and database of the Drosophila nervous system	Database : Annotation	Web		June 24, 2010	Home Page
SOURCE	SOURCE is a unification tool which dynamically collects and compiles data from many scientific databases	Database : Annotation	Web		June 24, 2010	Home Page
PANDORA	Detect subsets of proteins that share unique biological properties	Tool : Protein Annotation	Web		June 24, 2010	Home Page
NetAffx	Affymetrix annotation database for all microarray products, free login required	Database : Microarray Annotation	Web		June 24, 2010	Home Page
Taverna	Taverna is an open source tool for designing and executing workflows	Tool : Integrated Analysis	Web		June 24, 2010	Home Page
Gaggle	A framework for exchanging data between independently developed software tools	Tool : Integrated Analysis	Web		June 24, 2010	Home Page
ADAPT	ADAPT describes the many-to-many relationships between Affymetrix™ probesets transcripts and genes	Database : Microarray Annotation	Web		June 24, 2010	Home Page
SmudgeMiner	Regional biases in Affymetrix chips	Tool : Microarray	Web		June 24, 2010	Home Page
arrayCGHbase	ArrayCGHbase is a comprehensive analysis platform for microarray based comparative genomic hybridisation	Database : Chromosomal : aCGH	Web		June 24, 2010	Home Page
ISACGH	ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling	Chromosomal : Tool : aCGH : Gene Expression	Web		June 24, 2010	Home Page
CAPweb	Copy Number Analysis Software on the Web aCGH software	Chromosomal : Tool : aCGH	Web		June 24, 2010	Home Page
Mitelman breakpoint database	Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer	Database : Genomic Aberration : Chromosomal	Web		June 24, 2010	Home Page