Specialized Sequence Databases

Database for Expressed Sequence Tags (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. For more information visit: http://www.ncbi.nlm.nih.gov/dbEST/index.html Database of Sequence Tagged Sites (dbSTS): dbSTS is an NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. For more information visit: http://www.ncbi.nlm.nih.gov/dbSTS/index.html Protein motifs: The library of predefined protein motifs can be indirectly obtained by DNA sequence or protein database. For more information visit: http://alces.med.umn.edu/pmotif.html Cloning Vectors: data base of Cloning Vectors from NCBI. For more information visit:http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=28384 Genome Mapping Databases Berkeley Drosophila Genome Project: The Berkeley Drosophila Genome Project (BDGP) is a consortium of the Drosophila Genome Center, funded by the National Human Genome Research Institute, National Cancer Institute, and Howard Hughes Medical Institute, through its support of work in the Gerald Rubin and Allan Spradling laboratories. 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. In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community. For more information visit: http://www.fruitfly.org/ Genetic Information for Eukaryotic Organisms (euGenes): euGenes provides a common summary of gene and genomic information from eukaryotic organism databases. This includes Gene symbol and full name; Chromosome, genetic and molecular map information; Gene product information (function, structure, and homologies) and Links to extended gene information. For more information visit: http://iubio.bio.indiana.edu:8089/ Human Genome: Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on eukaryotic genomes. Ensembl presents up-to-date sequence data and the best possible automatic annotation for eukaryotic genomes. In the context of the completion of the "Working Draft" of the Human Genome Sequence by the public Human Genome Project, Ensembl provided some URLs that are good starting points for working with the data. For ease of access, Ensembl have created a master web site called "Human Genome Central" containing a brief listing of links to some of the most useful public resources; further links to additional sites can be found within them. The web sites will be regularly updated with new information. Human Genome Central can be found on both the NCBI and EBI sites at: www.ncbi.nlm.nih.gov/genome/central www.ensembl.org/genome/central Human Genome Data Base: Established at Johns Hopkins University in Baltimore, Maryland, USA in 1990, the Genome Database (GDB) is the official central repository for genomic mapping data resulting from the Human Genome Initiative. At present, GDB comprises descriptions of the following types of objects: a. Regions of the human genome, including genes, clones, amplimers (PCR markers), breakpoints,cytogenetic markers,fragile sites,ESTs,syndromic regions,contigs and repeats. b. 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. c. Variations within the human genome including mutations and polymorphisms, plus allele frequency data. For more information visit: http://gdbwww.gdb.org/ Genome Database of the Mouse (GBASE): The Mouse Genome Database (MGD) contains information on mouse genetic markers, molecular segments, phenotypes, comparative mapping data, experimental mapping data, and graphical displays for genetic, physical, and cytogenetic maps. MGD is updated daily. For more information visit: http://www.informatics.jax.org/ Saccharomyces Genome Database (SGD): SGDTM 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. For more information visit: http://genome-www.stanford.edu/Saccharomyces/ Plant Genome Databases: Maize Genome Database ( MaizeDB): MaizeDB is a public Internet gateway to current knowledge about the maize genome and its expression. For more information visit: http://www.agron.missouri.edu/top.html Arabidopsis thaliana Database: The Arabidopsis Information Resource (TAIR) provides a comprehensive resource for the scientific community working with Arabidopsis thaliana, a widely used model plant. TAIR is collaboration between the Carnegie Institution of Washington Department of Plant Biology, Stanford, California, and the National Center for Genome Resources (NCGR), Santa Fe, New Mexico. Funding is provided by the National Science Foundation. For more information visit: http://www.arabidopsis.org/home.html Biological Culture and Stock Collection Databases American type Culture Collection (ATCC): ATCC is a global nonprofit bioresource center that provides biological products including microbial cultures, technical services, and educational programs to private industry, government, and academic organizations around the world. Its mission is to acquire, authenticate, preserve, develop, and distribute biological materials, information, technology, intellectual property, and standards for the advancement, validation, and application of scientific knowledge. E. coli Genetics Stock Center (CGSC): The CGSC Database of E.coli genetic information includes genotypes and reference information for the strains in the CGSC collection, gene names, properties, and linkage map, gene product information, and information on specific mutations. The CGSC Collection consists primarily of genetic derivatives of E. coli K-12, the non-pathogenic laboratory strain used in genetic and molecular studies, and includes combinations of 2-29 mutations from among 3500 mutations at more than 1000 different loci. For more information visit: http://cgsc.biology.yale.edu/ Microbial Germplasm Database: Microbial Germplasm Database (MGD) is a shared database of information on collections of microbial germplasm maintained primarily for research purposes, in laboratories in universities, in private industry, at USDA research field stations, and in NSF supported collections. For more information visit: http://mgd.nacse.org/hyperSQL/mgd/html/Info.html Enzymes and Metabolic Pathways Database KEGG: Kyoto Encyclopedia of Genes and Genomes (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. The KEGG project is undertaken in the Bioinformatics Center, Institute for Chemical Research, Kyoto University with supports from the Ministry of Education, Culture, Sports, Science and Technology and the Japan Society for the Promotion of Science. For more information visit: http://www.genome.ad.jp/kegg/java/metabolism.html EMP Project: Enzymes and Metabolic Pathways database, EMP, is a unique and most comprehensive electronic source of biochemical data. It covers all aspects of enzymology and metabolism and represents the whole factual content of original journal publications. The database format has about 300 subject fields to encode the following categories: For more information visit: http://www.empproject.com/about/ Rebase: The Restriction Enzyme Database is a collection of information about restriction enzymes, methylases, the microorganisms from which they have been isolated, recognition sequences, cleavage sites, methylation specificity, the commercial availability of the enzymes, and references - both published and unpublished observations(dating back to 1952). For more information visit: http://rebase.neb.com/rebase/rebase.html Prolysis: Welcome to PROLYSIS home page, intended as a Web resource for those interested in proteases and their natural or synthetic inhibitors. This page contains informations of general interest as well as useful links to other Internet resources. This Page has been created by Dr. Thierry MOREAU, Laboratory of Enzymology and Protein Chemistry, University François RABELAIS, TOURS, France and is maintained by Dr. Hervé CHOPLIN, University of Tours.