Genomic Databases

Organism(s) Database Site Descriptions
Comprehensive:
  • Mammals
  • Plants
  • Model organisms
Ensembl logo Ensembl
Mammals UCSC logo UCSC Genome Browser
Comprehensive:
  • Bacterial
TIGR logo 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 GDB *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 HGR logo 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) MGI logo Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.
Rat RGD logo 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 logo 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 logo 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) BDGP logo 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 logo 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 logo 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 tair logo 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 logo 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 from Japan
SOURCE logo 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

swissprot logo 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.
PIR logo An integrated public resource of protein informatics to support genomic and protemic research and scientific discovery.
PDB logo The single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.
CATH logo 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).


Protein Interactions Database

BIND logo 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.
DRC logo Database of Ribosomal Crosslinks (DRC)
DIP logo The DIPTM database
NPIDB DNA-Protein Interaction Data Base
DPInteract logo 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.For 55 E. coli DNA-binding proteins with known binding sites, we have compiled DNA-binding site matrices and performed searches over the complete E. coli K12 genome.
HPID logo Human Protein Interaction Database
Hybrigenics logo 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 logo 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 logo JenPep Database
MINT logo 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'.
MPID logo 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 logo PathCalling Yeast Interaction Database
MINT logo 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
ProNIT logo Thermodynamic Database for Protein
logo Protein-Nucleic Acid Recognition Databases and Tools is a system to help researchers understand the mechanism of nucleic acid recognition by proteins.
SPiD logo Subtilis Protein interaction Database
the GRID logo 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 logo 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.
LOC3d logo 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 logo NLSdb is a database of nuclear localization signals (NLSs) and of nuclear proteins targeted to the nucleus by NLS motifs.
NOPdb Welcome to the Nucleolar Proteome Database. This site contains all of the data from our ongoing proteomic analysis of human nucleoli, which is carried out as a collaboration between the Lamond and Mann laboratories. Using high sensitivity mass spectrometry and stringent criteria, we have so far identified ~700 human nucleolar proteins. More recently, we used a quantitative proteomic approach for the temporal characterization of protein flux through the nucleolus, determining the kinetics of up to 489 nucleolar proteins after various drug treatments and demonstrating that there is no unique, complete proteome for the nucleolus, but rather an overlapping set of proteomes that are relevant to different cell states or conditions. The data can be searched in a variety of ways (see below). To find out more about the nucleolus, our various proteomics studies, the SILAC method of quantitative proteomics or the structure of this database, follow the appropriate links. For a downloadable PDF file listing all of the proteins alphabetized by name, click here. The same table is available with the proteins sorted by molecular weight by clicking here.
SPD Based on a bioinformatic ...ecreted Protein Database.