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Biological Databases

     

Biological Databases are like any other databases. Biological Database contains the sequence data of DNA, RNA etc.. These database are organized for optimal retrieval and analysis.

Here are the links of biological databases:

Biological Database Links

• NCBI Home
  Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease.
    
• Entrez Search and Retrieval System
  Entrez Programming Utilities are tools that provide access to Entrez data outside of the regular web query interface and may be helpful for retrieving search results for future use in another environment.
   
• KEGG: Kyoto Encyclopedia of Genes and Genomes
  A grand challenge in the post-genomic era is a complete computer representation of the cell and the organism, which will enable computational prediction of higher-level complexity of cellular processes and organism behaviors from genomic information. Towards this end we have been developing a bioinformatics resource named KEGG, Kyoto Encyclopedia of Genes and Genomes, as part of the research projects in the Kanehisa Laboratory of Kyoto University Bioinformatics Center. 
   
• TIGR Gene Indices
  The TIGR Gene Index Project is supported in part by funding from the US Department of Energy, Grant #DE-FG02-99ER62852, and the US National Science Foundation, Grant #DBI-9983070. Additional funds are provided by the US National Science Foundation through grants #DBI-9813392 and #DBI-9975866.
   
• Gramene: A Comparative Mapping Resource for Grains
  Gramene is a curated, open-source, Web-accessible data resource for comparative genome analysis in the grasses. Our goal is to facilitate the study of cross-species homology relationships using information derived from public projects involved in genomic and EST sequencing, protein structure and function analysis, genetic and physical mapping, interpretation of biochemical pathways, gene and QTL localization and descriptions of phenotypic characters and mutations.
   
• MaizeDB
  The goals of this project are to provide a central repository for public maize information and present it in a way that creates intuitive biological connections for the researcher with minimal effort as well as provide a series of computational tools that directly address the questions of the biologist in an easy-to-use form.
   
• Barley Genomics10pt
  AREAS Of RESEARCH: Barley Genome Mapping , Map-Based Cloning, Molecular Breeding, Mutant Isolation & Characterization, Functional Genomics, BAC Address Calculator, Developmental Mutants 
   
• EMBL European Bioinformatics Institute10pt
  The European Bioinformatics Institute (EBI) is a non-profit academic organisation that forms part of the European Molecular Biology Laboratory (EMBL). The EBI is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures.
   
• A Catalog of Genes for Plant Glycerol Lipid Biosynthesis
  The current version of this catalog contains more than 2600 sequence files, many of them with annotation and results of our analysis. This version is updated as of Aug. 1999 and includes essentially all publicly available genomic, cDNA, EST and GSS sequences for 62 plant polypeptides involved in lipid metabolism in higher plant species. An important feature of the catalog are the multiple alignments of amino acid sequences deduced from genomic and EST sequences. This version of the dataset accounts for approximately 70% of the Arabidopsis genome. 
   
• Grain Genes: A Small Grains and Sugarcane Database
  10ptGBrowse, developed by the GMOD group, is a Genome Browser that provides a wealth of genome annotation for maps in the GrainGenes collection. Users can easily manipulate the view of the chromosome and type of data displayed.
   
• PathDB Pathways
  PathDB is a beta level research tool for scientists interested in analyzing their experimental or computational data in the context of biological pathways and networks.
   
• Enzymes and Metabolic Pathways Database
  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.
    
• Boehringer Mannheim Biochemical Pathways
  Roche Applied Science: LightCycler, MagNA Pure LC, Lumi-Imager, PCR
   
• ExPASy Molecular Biology Server
  The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE.
    
• Nucleic Acids Research:2000 Biological Database Issue 
  Nucleic Acids Research (NAR) publishes the results of leading edge research into physical, chemical, biochemical and biological aspects of nucleic acids and proteins involved in nucleic acid metabolism and/or interactions. It enables the rapid publication of papers under the following categories: chemistry, computational biology, genomics, molecular biology, RNA and structural biology. A Survey and Summary section provides a format for brief reviews. The first issue of each year is devoted to biological databases, and an issue in July is devoted to papers describing web-based software resources of value to the biological community.
   
• Yeast Protein Database HOME PAGE
  Six database volumes of biological information about proteins comprise Incyte's Proteome BioKnowledge Library. Each volume focuses on a different organism important in pharmaceutical research.
    
• Saccharomyces Genome Database
  SGD^TM 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.
    
• The Breast Cancer Gene Database
  A database of genes involved in breast cancer. It is similar to the Tumor Gene Database (below) but limited in scope to those genes involved in human breast cancer and thus will be able to go into greater depth. The criteria for a gene to be included in this database are that it has been shown to be involved in human breast cancer (rather than an animal model) and that there is some evidence that it plays a functional role in the induction or progression of breast cancer.
    
• The Mammary Transgene Interactive Database
  This is an interactive database of literature on research designed to target transgene proteins to the mammary gland. Current emphasis is on biotechnology applications. Addition of tumor model and developmental model literature is planned.
    
• The Small RNA database
  Small RNAs are broadly defined as the RNAs not directly involved in protein synthesis. These are grouped under three categories: l) Capped small RNAs; 2) Noncapped small RNAs; and 3) Viral small RNAs. Sequences and references are included, and you can do wais searching with a keyword.
   
• The Tumor Gene Database
  A database of genes associated with tumorigenesis and cellular transformation. This database includes oncogenes, proto-oncogenes, tumor supressor genes/anti-oncogenes, regulators and substrates of the above, regions believed to contain such genes such as tumor-associated chromosomal break points and viral integration sites, and other genes and chromosomal regions that seems relevant.
   

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