Nucleic acid secondary databases

TABLE 15.8 Some nucleic acid secondary databases... 

Nucleic acid secondary databases Computational genomic serves ... 

Dwight, S.S., Harris, M.A., Dolinski, K., Bell, C.A., Binkley, G., Christie, K.R., Fisk, D.G., Issel-Tarver, L., Schroeder, M., Sherlock, G., Sethuraman, A., Weng, S., et al. 2002. Saccharomyces genome database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res. 30, 69-72. 

Although this chapter is about the GenBank nucleotide database, GenBank is just one member of a community of databases that includes three important protein databases SWISS-PROT, the Protein Information Resomce (PIR), and the Protein DataBank (PDB). PDB, the database of nucleic acid and protein structures, is described in Chapter 5. SWISS-PROT and PIR can be considered secondary databases, curated databases that add value to what is already present in the primary databases. Both SWISS-PROT and PIR take the majority of their protein sequences from nucleotide databases. A small proportion of SWISS-PROT sequence data is submitted directly or enters through a journal-scanning effort, in which the sequence is (quite literally) taken directly from the published literature. This process, for both SWISS-PROT and PIR, has been described in detail elsewhere (Bairoch and Apweiller, 2000 Barker et al., 2000.)... 

Nucleic acid and protein sequence analysis, including secondary structure prediction. GenBank, EMBL, SWISS-PROT, PIR, PROSITE, NASITE, and Vector-Bank databases on CD-ROM. Macintosh. PC/GENE for sequence analysis on PCs. IntelliGenetics Suite Sequence Analysis Software and GENESEQ database with patented protein and nucleic acid sequences. Sun and VAX. 

The Protein Data Bank (PDB) at Brookhaven National Laboratory is a database containing experimentally determined, three-dimensional structures of proteins, nucleic acids, and other biological macromolecules. The PDB has a history of service starting in 1971 to a global community of researchers, educators, and students in a variety of scientific disciplines. The archives contain atomic coordinates, bibliographic citations, primary and secondary structure information, as well as crystallographic structure factors and NMR experimental data. Scientists around the world contribute structures to the PDB and use it on a daily basis. The common interest shared by this community is a need to access information that can relate the biological functions of macromolecules to their three-dimensional structures. 

This chapter presents several techniques used in chemical ecology. In recent years, improvements in computational tools have allowed for more in-depth analyses of secondary metabolites and nucleic acids. These approaches often produce big data, making important automatic correlations wifti online databases. Based on performances of chemical analysis, major technical innovations have also emerged in imaging. It is, therefore, increasingly common to illustrate a given molecule with a resolution approaching the order of micrometers. This chapter presents these aspects as well as several possible axes of innovation. 

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