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Table 2.5. Major sequence databases accessible through the Internet
1. GenBank at the National Center for Biotechnology Information, National Library of Medicine, Washington, D.C. accessible from:
2. European Molecular Biology Laboratory (EMBL) Outstation at Hixton, England
3. DNA DataBank of Japan (DDBJ) at Mishima, Japan
4. Protein International Resource (PIR) database at the National Biomedical Research Foundation in Washington, D.C. (see Barker et al. 1998), an annotated protein database
5. The SwissProt protein sequence database at ISREC, Swiss Institute for Experimental Cancer Research in Epalinges/Lausanne, an annotated protein database
6. The Sequence Retrieval System (SRS) at the European Bioinformatics Institute allows both simple and complex concurrent searches of one or more sequence databases. The SRS system may also be used on a local machine to assist in the preparation of local sequence databases.
    The databases are available at the indicated addresses and return sequence files through an Internet browser. Many of the sites shown provide access to multiple databases. The first three database centers are updated daily and exchange new sequences daily, so that it is only necessary to access one of them. Additional Web addresses of databases of protein families and structure, and genomic databases, are given in Chapters 10 and 11. These databases can also provide access to sequences of a protein family or organism.
    The annotated protein data banks traditionally examine the scientific literature for physical evidence that the protein is actually produced in cells. The presence of mRNA sequences reveals that the gene is expressed but do not reveal whether or not the mRNA is translated into a protein. However, some proteins may be difficult to detect because they are made in small quantities, in specific cells or tissues, or at a particular time in development. Codon use by the mRNA of suspect genes can be examined for consistency with codon use by other genes that are known to be translated, as discussed in Chapter 9.


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