NCBI HandBook

The 'NCBI instruction manual' is an indispensible advisor to 1 of the world's richest and most vital bioinformatics web content, the U.S. nationwide heart for Biotechnology info at www.ncbi.nlm.nih.gov.

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The top of the page serves as a header and reports a variety of identifying information, including the name and description of the CD, other related CDs with links to their summary pages, as well as the source database, status, and creation date of the CD. A taxonomic node link (Taxa:)launches the Taxonomy Browser, whereas a Proteins (Proteins:)link uses CDART to show other proteins that contain the CD. Below the header is the interface for viewing the CD alignment, which can be done either graphically with Cn3D (if the CD contains a sequence with structural data) or in HTML, text, or mFASTA format.

Links Between Structure and Other Resources Integration with Other NCBI Resources As illustrated in the sections above, there are numerous connections between the Structure resources and other databases and tools available at the NCBI. What follows is a listing of major tools that support connections. Entrez Because Entrez is an integrated database system (Chapter 14), the links attached to each structure give immediate access to PubMed, Protein, Nucleotide, 3D Domain, or Taxonomy records. BLAST Although the BLAST service is designed to find matches based solely on sequence, the sequences of Structure records are included in the BLAST databases, and by selecting the PDB search database, BLAST searches only the protein sequences provided by MMDB records.

Tax ID List. Shows only the taxids of the taxa. This view can be used to download taxid lists from Entrez. Info. Shows a summary of most of the information associated with each taxon in the Taxonomy database (similar to the TaxBrowser taxon-specific display; Figure 3). This can be downloaded as a text file; an XML representation of these data is under development. Common Tree. A special display that shows a skeleton view of the relationships among the selected set of taxa and is described in the section below.

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