Composite and Specialized databases
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The document discusses composite and specialized databases, highlighting their functions and examples. Composite databases, like owl and nrdb, compile and filter sequence data from primary databases, while specialized databases focus on specific subject areas or formats. Additionally, rebase is introduced as a comprehensive database for restriction enzymes and their characteristics.
Composite and Specialized databases
- 2. Composite Database • It compile and filter sequence data from primary database. • More exhaustive (consider all elements) than individual databases. • Include protein sequence data from translated coding regions in DNA sequence databases. • Example: OWL, NRDB, BioSilico
- 3. OWL • Translation from nucleic acid sequences. • Sequences extracted from PIR, SWISS-PROT, PDB (Primary databases). • Redundancy is avoided by comparison of sequences, with the elimination of exact duplicates.
- 4. NRDB • NRDB is Non-redundant Database. • Non-redundancy is maintained by filtering multiple data from different primary database sources. • The database is similar in content to OWL, but contains more up-to- date information. • It is not non-redundant actually, but non-identical - i.e., only identical sequence copies are removed from the database. • As a result, NRDB is larger and less efficient to search than OWL. • To be rigorous, it is sensible to search NRDB, but for the purposes of a short tutorial, it is more practical to search OWL.
- 5. BioSilico • BioSilico is a web-based database system that facilitates the search and analysis of metabolic pathways. • Heterogeneous metabolic databases including LIGAND, ENZYME, EcoCyc and MetaCyc are integrated in a systematic way, thereby allowing users to efficiently retrieve the relevant information on enzymes, biochemical compounds and reactions. • In addition, it provides well-designed view pages for more detailed summary information. BioSilico is developed as an extensible system with a robust systematic architecture.
- 6. Specialized Database A specialized database—often called a research or library database—allows targeted searching on one or more specific subject areas (i.e., engineering, medicine, Latin American history, etc.), for a specific format (i.e., books, articles, conference proceedings, video, images), or for a specific date range during which the information was published. There are several types of specialized databases, including: • Bibliographic – details about published works • Full-text – details plus the complete text of the items • Multimedia – various types of media, such as images, audio clips, or video excerpts • Directory – brief, factual information • Numeric – data sources • Product – model numbers, descriptions, etc. • Mixed – a combination of other types, such as multimedia and full-text
- 7. REBASE • REBASE is known as Restriction Enzyme Database. • REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction–modification (R–M). • It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. • Isoschizomers are pairs of restriction enzymes specific to the same recognition sequence. • Neoschizomers are restriction enzymes that recognize the same nucleotide sequence as their prototype but cleave at a different site.