Sequence Neighbors link

The data are collected daily from a number of sources, including the National Center for Biotechnology Information (NCBI) and Gene Ontology (GO) Consortium. The warehouse includes sequences, structures, and complete genomes from Gen-Bank as well as annotation links such as NCBI taxon database terms, redundant sequences, sequence neighbors, conserved domains, Online Mendehan Inheritance in Man identifiers, GO terms, LocusLink identifiers, and PubMed links. 

MMDB s Web interface provides a Structure Smnmary page for each MMDB structure record, as shown in Figure 5.4. MMDB Structure Summary pages provide the FASTA-formatted sequences for each chain in the structure, links to MEDLINE references, links to the SDBAtlas record and the Brookhaven PDB site, links to protein or nucleic acid sequence neighbors for each chain in the structure, and links to VAST structure-structure comparisons for each domain on each chain in the structure. 

Figure 5.4. Structure query from NCBI with the structure IBNR (Bycroft et al., 1991). The Structure Summary links the user to RCSB through the PDB ID link, as well as to validated sequence files for each biopolymer, sequence, and three-dimensional structure neighbors through the VAST system. This system is more efficient than the RCSB system (Fig. 5.2) for retrieval because visualization, sequence, and structure neighbor links are made directly on the structure summary page and do not require fetching more Web pages.

Work out which operations each object must invoke on its neighbors, beginning with the head object, to achieve the after situation. To stick to basic design, your messages should only follow links. Draw them on top of the snapshot. It usually helps to number them in sequence of occurrence. Also number creations and deletions (see Figure 16.8). 

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