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Molecular Biology & Genetics Databases

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Featured sites: Nucleic Acids Research's January 1, 2000 issue Features articles on several dozen molecular biology & genetics databases. The online version of this issue features links to all the databases as well as helpful guides. Choose the HTML version of each article if you want to use the links. (NAR Online is restricted to UC users). DNASYSTEM Sequence Analysis Site From the Biology Department at UCSD. This site "provides Web links for nucleic acid and protein sequence analysis, and links to other molecular biology tools, as well as links to UCSD genome analysis resources." National Center for Biotechnology Information (NCBI) The following services are available - click links below for direct access... ENTREZ - search nucleotides, proteins, 3D structures, genomes, taxonomy, and MEDLINE through PubMed. BLAST- NCBI's sequence similarity search tool designed to support analysis of nucleotide and protein databases. NCBI Taxonomy Database Online Mendelian Inheritance in Man (OMIM) - catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues. Structure - the Molecular Modeling Data Bank.

Biological Macromolecules Crystallization Database Structures and crystallization conditions for 3500+ entries from 2500+ biological macromolecules. From the U.S. National Institute of Standards and Technology. Biologist's Control Panel A useful collection of databases compiled by the Baylor College of Medicine Genome Center. Database of Genome Sizes Provides comparative information on the genomes of various organisms, as well as data on how much of each genome has been sequenced to date. dbBrowser Provides facilities for interrogating the OWL composite sequence database and its derived database of fingerprints, PRINTS. It also provides links to a variety of other data sources: e.g. SWISS-PROT, PIR, GenBank, NRL-3D, PROSITE, ProDom, BLOCKS, SBASE, GCRDb, etc.; and to numerous sites and analysis tools: e.g. ExPASy, GenomeNet, SRS, SEQNET, EBI, etc. Part of EMBNet. The Deambulum Organized database location tool - browse by organism, type of sequence. From InfoBioGen, a French national bioinformatics center. EC Enzyme Database ExPASy Molecular Biology Server Search SWISS-PROT and many other databases. FlyBase FlyBase is a database of genetic and molecular data for Drosophila, and is supported by NIH and the British Medical Research Council. GenBank GenBank is the NIH genetic sequence database, a collection of all known DNA sequences. Genome Data Base (GDB) The database has been officially terminated, but its operation has been extended into 1999 to ensure a smooth transition to its successor. Genomes On-Line Database (GOLD) Resource for comprehensive access to information regarding complete and ongoing genome projects around the world. Read more about it in Kyrpides N. Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide. Bioinformatics 1999 Sep; 15(9):773-4 HIV Sequence Database HPV (Human Papillomaviruses) Sequence Database Human 2-D PAGE View protein information by clicking various spots on gel images. Human and mouse databases are available, as well as information on lab procedures and images of gels from various animal species. KLOTHO Database on biochemical compounds with structures in .gif and 3D formats. Kyoto Encyclopedia of Genes & Genomes (KEGG) Features databases of metabolic and regulatory pathways, with information on genes that control them. ModBase: A Database of Comparative Protein Structure Models The database currently contains 3D models for substantial segments of 15-23% of proteins in the genomes of M. genitalium, M. jannaschii, E. coli, S. cerevisiae, and C. elegans. In total, there are models for 3,732 proteins. Information about the modelling process used can be found in Roberto Sánchez and Andrej Sali. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. PNAS 1998; 95(23): 13597-13602. Nucleic Acid Database Site also features a structure finder, the macromolecular crystallographic information file (mmCIF), and à la mode, an "environment for building models of ligand and monomer molecular components". Protein Data Bank (PDB) From the Research Collaboratory for Structural Bioinformatics, this is an international repository for the processing and distribution of 3-D macromolecular structure data. As of July 1999, the PDB component of the RCSB's work resides at the San Diego Supercomputer Center. PUMA Data on metabolic pathways, alignments, and phylogenetic trees for organisms currently being used as models in genome research. RNA WWW Server Several RNA-related databases. SALSA Search many different DNA and protein sequence databases using one interface.

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