Bioinformatics & Genomics
Cell Biology & Metabolism
Gene Expression & Information
Proteins & Other Biological Molecules
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AGR: Arabidopsis Genome Resource
[UK CropNet] An information resource aimed to integrate sequence data with physical genetic maps of Arabidopsis within the UK CropNet project and provide information for identifying gene function and crop plant orthologues of Arabidopsis genes.
Arabiodopsis Information Resource
[NCGR and the Carnegie Institution] TAIR provides literature and genomic data about the plant Arabidopsis thaliana .
ARS Genome Database Resource
[USDA-ARS Center for Agricultural Bioinformatics, Cornell University ] A site with plant genome databases and information. Included are plant genes, chromosome maps, DNA fingerprints, beneficial traits, and crop varities that possess query traits.
Berkeley Drosophila Genome Project
[Univ. of California, Berkeley] (BDGP) A comprehensive site with information on the fruit fly and its genome-related projects, and links to gene and genome analysis tools.
[SRI International] The BioCyc Knowledge Library is the new name for EcoCyc and MetaCyc. It is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism, with the exception of the MetaCyc database, which is a reference source on metabolic pathways from many organisms.
[Osaka University] A human and mouse gene expression data bank, collecting quantitative and qualitative information on gene expression.
Center for Agricultural Bioinformatics System
[USDA-ARS] The CAB provides curation and delivery of agricultural genomic data and resources while fostering research and development of novel approaches in agricultural bioinformatics.
CGAP: Cancer Genome Anatomy Project
[National Cancer Institute and NCBI] Intends a comprehensive molecular characterization of normal, precancerous, and malignant cells.
CGSC: E. coli Genetic Stock Center
[Yale University] A database of genetic information, including genotypes and reference information for the strains in the CGSC collection, gene names, properties, linkage map, gene product information, and information on specific mutations.
[USDA-ARS Center for Bioinformatics and Comparative Genomics ] Provides full descriptions of all
cultures in the Chlamydomonas Genetics Center collection, all the literature citations, GenBank accessions, and much more.
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CUTG: Codon Usage Tabulated from GenBank
[National Institute of Genetics] Codon usage in individual genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Database. The compilation of codon usage is synchronized with each major release of GenBank.
[Kazusa DNA Research Institute] The genome database for Synechocystis sp. strain PCC6803.
dbEST: Expressed Sequence Tags database
[The National Center for Biotechnology Information] 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.
DOGS: Database of Genome Sizes
[Center for Biological Sequence Analysis] A comprehensive list of (estimated) genome sizes for different organisms. Both the completed and estimated genomes are listed. The estimated genome sizes are given for both the organisms currently being sequenced and those for which no sequencing program is in progress.
ECDC: E. coli Database Collection
[Univ. of Giessen] A site dedicated to the E. coli K-12 chromosome.
Eukaryotic Promoter Database
[ISREC] An annotated non-redundant collection of eukaryotic POL II promoters, for which the
transcription start site has been determined experimentally.
[Westfalische Wilhelms-Universitat Munster, Germany] An image-based database on development and genetics, especially on expression patterns of genes (enhancer trap lines, cloned genes).
Gene Expression in Tooth
[The Tooth Development Group of the Developmental Biology Programme, University of Helsinki, Finland] Information about expression of different genes in the developing tooth with a graphical form of data presentation.
[Home Journal Library Index] Presents data describing the mouse phenotypes rendered by the knockout of genes coding for the various molecules contained within the database.
[Weizmann Institute of Science ] GeneCards is a database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol, as well as selected others.
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Genome Sequencing Projects
[Argonne National Laboratory and TIGR] Links to many genome sequencing projects and databases, which gives the current status of the different projects.
GenomeNet WWW server
[Institute for Chemical Research, Kyoto University] A Japanese network of database and computational services for genome research and related research areas in molecular and cellular biology.
Genomes On Line Database
[Integrated Genomics Inc.] (GOLD) GOLD is a World Wide Web resource for comprehensive access to information regarding complete and
ongoing genome projects around the world.
[Cambridge Healthtech Institute] "Genomics knowledge and insights are expanding exponentially.
Genomics Glossaries help you keep abreast of evolving and interdisciplinary vocabulary." This site has a large number of glossaries ranging from introductory to advanced in genomics and related areas.
[GEN Research Institute & Human Genome Center] A human cDNA database achieved through a large-scale human cDNA analysis project containing sequence information and data concerning chromosomal localizations and expression patterns.
HGMD: Human Gene Mutation Database
[Institute of Medical Genetics in Cardiff] Represents an attempt to collate known (published) gene lesions responsible for human inherited disease comprised of various types of mutation within the coding regions of human nuclear genes.
HTDB: Human Transcript Database
[Human Genome Sequencing Center, Baylor College of Medicine] A curated source for information related to RNA molecules that have been sequenced. The goal of HTD is to provide a clone-based platform that represents as many of the human transcripts that have been sequenced as possible.
ICN: Ion Channel Network
[University of Leicester, and the Center for Neuroscientific Databases at the University of Minnesota] Information on ion channel genes and proteins.
Induced Mutant Resource (IMR)
[The Jackson Laboratory] Database of transgenic and targeted mutant mice strains which provides information such as a description of the mutant phenotype, husbandry requirements, and genetic typing protocols.
[Society for Developmental Biology, Purdue University] Drosophila genes and their roles in development.
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Internet Autopsy Gene Link Database
[Jules Berman] (Association for Pathology Informatics) Database designed to work with the Internet Autopsy Database, permitting researchers to relate genetic data directly to disease entities.
Kidney Development Database
[Department of Anatomy, University of Edinburgh, Scotland] Contains data from developmental studies of the kidney and includes relevant genes and gene expression patterns.
Kyoto Encyclopedia of Genes and Genomes
[GenomeNet] "KEGG is an effort to computerize current knowledge of molecular and cellular biology in terms of the information pathways that consist of interacting molecules or genes and to provide links from the gene
catalogs produced by genome sequencing projects."
[Hospital Necker Enfants Malades] A database that currently contains information about the published mutations of the fibrillin gene FBN1. For each mutation, information is provided at several levels: the gene level, the protein level, and at the clinical level.
MGI: Mouse Genome Informatics
[The Jackson Laboratory] Provides integrated access to various sources for information on the genetics and biology of the laboratory mouse. MGI resource comprises the Mouse Genome Database (MGD), the Gene Expression Database (GXD), the Encyclopedia of the Mouse Genome (Encyclopedia), and related software and data.
NRSub: Non-Redundant B. subtilis database
[Pole Bio-Informatique Lyonnais] A database of sequences and information on the completed Bacillus subtilis genome.
OMIM: Online Mendelian Inheritance in Man
[National Center for Biotechnology Information] A catalog of human genes and genetic disorders.
Ortholog/Paralog Groups of Functional Units
[Institute for Chemical Research, Kyoto University] Conserved gene clusters in the KEGG metabolic and regulatory pathways.
[Béroud and Soussi] The p53 gene and its many mutations are found on this database. It includes tools for analysis of p53 mutations and carcinogenesis.
[Proteome, Inc.] This site allows access to proteome databases for yeast (YPD), S. pombe (PombePD), and C. elegans (WormPD). These databases contain genomic sequences, functional genomic, and other comprehensive organism information.
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Salivary Gland Development Database
[Department of Anatomy, University of Edinburgh, Scotland] Contains data from developmental studies of the human salivary gland including cell and molecular data, immune information, and gene expression data.
Sinai's Mammary Transgene Database
[Baylor College of Medicine] Summarizes the results of experiments in which transgenes are expressed in the mammary gland of experimental and agricultural animals. The database is searched according to four criteria: expressed sequences in the transgene, regulatory sequences in the transgene, species in which the transgene is expressed and the level at which the transgene was found to be expressed. In addition, the user can choose to consider expression in RNA, protein, activity or the portion of that activity which is secreted into milk.
[Cornell and Iowa State University] This database contains genomic and metabolic information for soybeans.
[Institut Pasteur] Database of DNA sequences, gene functions, and proteins from Bacillus subtilis.
[GBF] A database program that compiles data about gene regulatory DNA sequences; from this data programs have been developed to identify putative promoter or enhancer structures.
TransTerm: Translational Signal Database
[University of Otago] TransTerm is a database of sequence contexts about the stop and start codons of many species found in GenBank. TransTerm also contains codon usage data for these same species and summary statistics for the sequences analysed.
Tumor Gene Database
[Baylor College of Medicine] Contains information about genes which are targets for cancer-causing mutations, proto-oncogenes, and tumor suppressor genes with a goal to provide a standard set of facts about all known tumor genes.
UDB: The Unified Database for Human Genome Mapping
[WISGB] The UDB presents an integrated map for each human chromosome, based on
data integrated from various radiation hybrid, linkage and physical mapping resources. The
integrated map currently includes genes, STSs, and EST clusters.
Universal Mutation Database (Locus Specific)
[INSERM] Links to sites with software and databases for mutations in many human genes.
WormBase (Caenorhabditis elegans)
[CalTech, CSHL, WUSTL, The Sanger Center, and Le Centre National de la Recherche Scientifique of Fran] This is a repository of mapping, sequencing, and phenotypic information about the C. elegans nematode.
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