Databases Biological

Many biochemical databases with sophisticated topics have been developed for solving various problems. Since 1996 the first issue of each journal volume of Nucleic Acid Research has been reserved for the presentation of molecular biology databases [28]. A comprehensive catalog on the Internet is DBCAT, currently listing 511 databases [29, 30). 

Discala C, Benigni X, Barillot E, Vaysseix G. DBcat a catalog of 500 biological databases. Nucleic Acids Res 2000 28 8-9. 

Searching through Databases Applications of network BLAST server, 266, 131 Entrez molecular biology database and retrieval system, 266, 141 applying motif and profile searches,... 

Taboureau O, Nielsen SK, Audouze K et al (2011) ChemProt a disease chemical biology database. Nucleic Acids Res 39 D367-D372... 

It is not necessary to have a complete understanding of the Internet in order to tap into its vast resources. The fundamental concepts provided here will allow you to take advantage of two essential activities (1) biochemical literature searching and (2) using Web directories and biological databases. 

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. 

How do you find the different biological databases on the Internet In an effort to publicize the numerous sites that are being maintained, several Internet sites have been created to act as directories. Two of these database directories that we have found to be quite useful are the Biology Workbench (http //biology.ncsa.uiuc.edu) and Pedro s BioMolec-ular Research Tools (http //wwwl.iastate.edu/ pe-dro/research tools.html). 

Table VI-1 An Incomplete Listing of Biological Databases and Other Useful Sites on the World Wide Web...

SwissProt is a computational biology database specializing in protein sequence analysis maintained by the Swiss Federal Institute of Technology (ETH) in Zurich, Switzerland. Like the other general databases described above, a number of more specialized biological databases draw information from this source. 

The GENEMAN application is a tool that allows you to access and search for DNA and protein sequences located in six different biological databases. The search for a sequence of interest can be made as broad or restrictive as desired, since there are 12 different fields (definition, reference, source, accession number, etc.) to choose from when the search is performed. In addition to performing database searches to find sequences of interest, GENEMAN allows you to search the database for sequences that share homology with the sequence of interest, or for entries that contain a particular conserved sequence. Any number of different DNA or protein sequences found in these databases can be isolated and stored as a sequence file for later analysis. 

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