Databases

Genomic Databases

Organism(s)	Database Site	Descriptions
Comprehensive: - Mammals - Plants - Model organisms	emsembl	Ensembl
Mammals		UCSC Genome Browser
Comprehensive Bacterial	TIGR	The Institute for Genomic Research (TIGR) is a not-for-profit research institute whose primary research interests are in structural, functional and comparative analysis of genomes and gene products from a wide variety of organisms including viruses, eubacteria, archaea, and eukaryotes.
Human		*Regions of the human genome, including genes, clones, amplimers (PCR markers), breakpoints, cytogenetic markers, fragile sites, ESTs, syndromic regions, contigs and repeats. *Maps of the human genome, including cytogenetic maps, linkage maps, radiation hybrid maps, content contig maps, and integrated maps. These maps can be displayed graphically via the Web. *Variations within the human genome including mutations and polymorphisms, plus allele frequency data.
Human		NCBI's Web site serves an an integrated, one-stop, genomic information infrastructure for biomedical researchers from around the world so that they may use this data in their research efforts.
Mus musculus (Mouse)		Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.
Rat		The Rat Genome Database was created to serve as a repository of rat genetic and genomic data, as well as mapping, strain, and physiological information. It also facilitates investigators research efforts by providing tools to search, mine, and analyze this data.
Zebrafish		ZFIN serves as the zebrafish model organism database. The long term goals for ZFIN are a) to be the community database resource for the laboratory use of zebrafish, b) to develop and support integrated zebrafish genetic, genomic and developmental information, c) to maintain the definitive reference data sets of zebrafish research information, d) to link this information extensively to corresponding data in other model organism and human databases, e) to facilitate the use of zebrafish as a model for human biology and f) to serve the needs of the research community.
Drosophila (fruit fly)		FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila. It includes data from the Drosophila Genome Projects and data curated from the literature.
Drosophila (fruit fly)		The Berkeley Drosophila Genome Project (BDGP) is a consortium of the Drosophila Genome Center. The goals of the Drosophila Genome Center are to finish the sequence of the euchromatic genome of Drosophila melanogaster to high quality and to generate and maintain biological annotations of this sequence.
Saccharomyces Cerevisiae (Yeast)		SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.
Plants		PlantGDB is the homepage for the NSF-funded project "PlantGDB - Plant Genome Database and Analysis Tools" (PI: Volker Brendel). The goals of this project are [1] to set up annotated species-specific EST databases for all major plants and link the EST data to other biological information, [2] to establish inter-species query capabilities to allow cross-species comparisons, and [3] to provide web-accessible computational tools for gene identification and characterization.
Arabidopsis		The Arabidopsis Information Resource (TAIR) provides a comprehensive resource for the scientific community working with Arabidopsis thaliana, a widely used model plant. TAIR consists of a searchable relational database, which includes many different datatypes.
Maize (corn)		MaizeDB is a public Internet gateway to current knowledge about the maize genome and its expression. It has been continuously supported since 1991 by the USDA-ARS, and more recently also by the NSF and the University of Missouri.

Microarray Database

READ	Riken Expression Array Database
	SOURCE is a unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports.
Transcriptome informatics	Transcriptome databases

Proteomic Databases

	Swiss-Prot is a curated protein sequence database which strives to provide a high level of annotations (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases.
	An integrated public resource of protein informatics to support genomic and protemic research and scientific discovery.
	The single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.
	CATH is a novel hierarchical classification of protein domain structures, which clusters proteins at four major levels, Class(C), Architecture(A), Topology(T) and Homologous superfamily (H)./td>

Protein Interactions Database

	The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions. The contents of BIND include high-throughput data submissions and hand-curated information gathered from the scientific literature.
	Database of Ribosomal Crosslinks (DRC)
	The DIPTM database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data.
	DNA-Protein Interaction Data Base
	This database is copyright 1994 the President and Fellows of Harvard College. Robison, K., and Church, G. DPInteract: A database on DNA-protein interactions. (1994). http://arep.med.harvard.edu/dpinteract/ Electronically published and manuscript in preparation.
	Human Protein Interaction Database
	Hybrigenics identifies new drug targets and therapeutic molecules using a combination of high throughput protein interaction mapping, in-depth functional validation and leading-edge chemical screening technologies. Its mission is to discover and develop small molecule drug candidates that address unmet medical needs, primarily in Oncology. Hybrigenics gives access to its functional Yeast Two-Hybrid platform on a fee-for-service basis.
	iHOP - Information Hyperlinked over Proteins - A network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. A freely accessible information portal on interactions of genes and proteins extracted from PubMed.
	JenPep Database
	MINT is a relational database designed to store interactions between biological molecules. Presently, MINT focuses on experimentally verified protein interactions with special emphasis on proteomes from mammalian organisms. MINT consists of entries mined in the scientific literature by curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically through the 'MINT Viewer'.
	MHC-Peptide Interaction Database (MPID) provides structural information and characterization of MHC peptide interaction on major histocompatibility complex of both class I and class II.
	PathCalling Yeast Interaction Database
PDZBase	PDZBase is a manually curated protein-protein interaction database developed specifically for interactions involving PDZ domains. PDZBase currently contains 339 experimentally determined protein protein interactions.
PPI	Protein Protein Interaction Viewer
PPID	Protein Protein Interaction Database
	Thermodynamic Database for Protein
	Protein-Nucleic Acid Recognition Databases and Tools is a system to help researchers understand the mechanism of nucleic acid recognition by proteins.
	Subtilis Protein interaction Database
	General Repository for Interaction Datasets
YEAST protein complex database	Systematic analysis of multiprotein complexes in Saccharomyces cerevisiae, as a model system relevant to human.

Protein Subcellular Localization Database

	DBSubLoc is a database of protein subcellular localization. This database contains proteins from primary protein database SWISS-PROT and PIR. By collecting the subcellular localization annotation, these information are classified and categorized by cross referencs to taxonomies and Gene Ontology database.
	Database of predicted subcellular localization for eukaryotic proteins of known 3-D structure.
MitoRes	MitoRes, is a comprehensive and reliable resource for massive extraction of sequences and sub-sequences of nuclear genes and encoded products targeting mitochondria in metazoa. It has been developed for supporting high-throughput in-silico analyses aimed to studies of functional genomics related to mitochondrial biogenesis, metabolism and to their pathological dysfunctions.
NESbase 1.0	NESbase is a database of proteins in which the presence of Leucine-rich nuclear export signal (NES) has been experimentally verified.
	NLSdb is a database of nuclear localization signals (NLSs) and of nuclear proteins targeted to the nucleus by NLS motifs.
NOPdb	Nucleolar Proteome Database v 2.0
SPD	Based on a bioinformatic pipeline and manual check, we have developed a collection of secreted proteins from Human, Mouse and Rat proteomes, which includes sequences from SwissProt, Trembl, Ensembl and Refseq. Such a collection is named as SPD, Secreted Protein Database.