Primary databases

Herbicides are also sometimes classified according to mode of action, selectivity, registered uses, and toxicity. The ever-increasing importance of herbicides and other pesticides and agrochemicals to a wide range of users, regulators, and researchers has led to the development of multiple and extensive computer databases. The primary database resources contain collected information relevant to herbicides, and numerous resource pubHcations are available to those needing information on the various aspects of herbicides (2). 

The application of the primary databases and structural analytical tools will be introduced using a protein from a future experiment. In Experiment 4, you will extract, purify, and characterize a-lactalbumin from bovine milk. To prepare for this activity, here you will learn about the structure of a related protein, a-lactalbumin from humans. We will search databases to find and view its primary and secondary structure and also determine if there are other proteins with a similar amino acid sequence and structure. After completion of these exercises, you will be able to apply these computer tools to proteins of your own choice. 

Databases are electronic filing cabinets that serve as a convenient and efficient means of storing vast amounts of information. An important distinction exists between primary (archival) and secondary (curated) databases. The primary databases represent experimental results with some interpretation. Their record is the sequence as it was experimentally derived. The DNA, RNA, or protein sequences are the items to be computed on and worked with as the valuable components of the primary databases. The secondary databases contain the fruits of analyses of the sequences in the primary sources such as patterns, motifs, functional sites, and so on. Most biochemical and/or molecular biology databases in the public domains are flat-file databases. Each entry of a database is given a unique identifier (i.e., an entry name and/or accession number) so that it can be retrieved uniformly by the combination of the database name and the identifier. 

Retrieve one primary database of protein sequence and its secondary databases and discuss their relationships. 

DATABASE SEARCH AND SEQUENCE ALIGNMENT 11.2.1. Primary Database... 

There are different classes of protein sequence databases. Primary and secondary databases are used to address different aspects of sequence analysis. Composite databases amalgamate a variety of different primary sources to facilitate sequence searching efficiently. The primary structure (amino acid sequence) of a protein is stored in primary databases as linear alphabets that represent the constituent residues. The secondary structure of a protein corresponding to region of local regularity (e.g., a-helices, /1-strands, and turns), which in sequence alignments are often apparent as conserved motifs, is stored in secondary databases as patterns. The tertiary structure of a protein derived from the packing of its secondary structural elements which may form folds and domains is stored in structure databases as sets of atomic coordinates. Some of the most important protein sequence databases are PIR (Protein Information Resource), SWISS-PROT (at EBI and ExPASy), MIPS (Munich Information Center for Protein Sequences), JIPID (Japanese International Protein Sequence Database), and TrEMBL (at EBI). ... 

Table 2 Primary databases of the National Library of Medicine...

In broad terms, there are three different approaches in the collection and presentation of interaction data (1) primary databases, which include experimentally proven protein interactions coming from either small-scale or large-scale... 

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.)... 

Links. PDB s search engine, the Structme Explorer, can be used to retrieve PDB records, as shown in Figure 5.2. The Structure Explorer is also the primary database of links to third-party aimotation of PDB structure data. There are a number of links maintained in the Structure Explorer to Internet-based three-dimensional structure services on other Web sites. Figme 5.2 shows the Structure Summary for the protein bamase (IBNR Bycroft et al., 1991). The Structure Explorer also provides links to special project databases maintained by researchers interested in related topics, such as structural evolution (FSSP Holm and Sander, 1993), structure-structure similarity (DALI Holm and Sander, 1996), and protein motions (Gerstein et al., 1994). Links to visualization tool-ready versions of the structure are provided, as well as authored two-dimensional images that can be very helpful to see how to orient a three-dimensional structure for best viewing of certain features such as binding sites. 

TABLE 14.11 Some primary database sites of biochemical interest... 

Sequence databases generally specialize in one type of sequence data, i.e. DNA, RNA or protein (Higgins and Taylor, 2(XX)). Structure data must unambiguously define the atomic connectivities and the precise three-dimensional coordinates of all atoms within the molecule. These sequences and structures are the itans to be eomputed on and worked with as the valuable components of the primary databases. Generally, the gateways to sequence and structure databases include ... 

The DNA secondary databases offer analytical results (e.g. gene motifs, splice sties, transcription regulators) derived form the primary databases of INSDC, some of which are listed in Table 15.8. 

Another important aspect is how processed the information is in the database. Databases are often categorized as primary and secondary ones [74]. Primary databases contain only raw experimental results of a certain kind. As high-throughput technologies evolve in all fields of life sciences, the number of primary databases increases day to day. Secondary databases contain the analysis of raw data found in primary databases. Even if it is possible to calculate some of these parameters by analyzing the data... 

Anonymous (2008) Livestock primary database. PAOSTAT Web site. Food and Agriculture Organization of the United Nations, http //faostat.fao.org. Accessed 15 Jan 2011... 

Accident primary database, local indicators and secondary indicators... 

Secondary sequence databases (information extracted and summarized from primary databases) ... 

Structural data are stored in, and can be accessed from, three primary databases which are continually updated. Data for organic and metal-organic compounds and boranes are compiled by the Cambridge Structural Database (www.ccdc. cam.ac.uk), while crystallographic data for purely inorganic compounds (e.g. metal and non-metal halides and oxides) are deposited in the Inorganic Crystal Structure Database (www.fiz-karlsruhe.de). Structural data for biological macromolecules are collected in the Protein Data Bank (www.rcsb.org/pdb). 

In this article, the focus lies on databases on environmental information of chemical substances. It will be indicated in which primary database to find a particular kind of environmental information. Examples will be given on the quantity of environmental information stored in the databases described. 

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