Composite: It compile and filter sequence data from primary database. Specialized : database—allows targeted searching on one or more specific subject areas

1. 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.