Composite and Specialized databases

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 compileand filtersequence 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
•NRDBisNon-redundantDatabase.
•Non-redundancyismaintainedbyfilteringmultipledatafromdifferent
primarydatabasesources.
•ThedatabaseissimilarincontenttoOWL,butcontainsmoreup-to-
dateinformation.
•Itisnotnon-redundantactually,butnon-identical-i.e.,onlyidentical
sequencecopiesareremovedfromthedatabase.
•Asaresult,NRDBislargerandlessefficienttosearchthanOWL.
•Toberigorous,itissensibletosearchNRDB,butforthepurposesofa
shorttutorial,itismorepracticaltosearchOWL.

5. BioSilico
•BioSilicoisaweb-baseddatabasesystemthatfacilitatesthesearch
andanalysisofmetabolicpathways.
•Heterogeneous metabolic databases
includingLIGAND,ENZYME,EcoCycandMetaCycareintegrated
inasystematicway,therebyallowinguserstoefficientlyretrievethe
relevantinformationonenzymes,biochemicalcompoundsand
reactions.
•Inaddition,itprovideswell-designedviewpagesformoredetailed
summaryinformation.BioSilicoisdevelopedasanextensiblesystem
witharobustsystematicarchitecture.

6. Specialized Database
Aspecializeddatabase—oftencalledaresearchorlibrarydatabase—allowstargeted
searchingononeormorespecificsubjectareas(i.e.,engineering,medicine,Latin
Americanhistory,etc.),foraspecificformat(i.e.,books,articles,conference
proceedings,video,images),orforaspecificdaterangeduringwhichtheinformation
waspublished.
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
•REBASEisknownasRestrictionEnzymeDatabase.
•REBASEisacomprehensivedatabaseofinformationaboutrestriction
enzymes,DNAmethyltransferasesandrelatedproteinsinvolvedinthe
biologicalprocessofrestriction–modification(R–M).
•Itcontainsfullyreferencedinformationaboutrecognitionand
cleavagesites,isoschizomers,neoschizomers,commercialavailability,
methylationsensitivity,crystalandsequencedata.
•Isoschizomersarepairsofrestrictionenzymesspecifictothesame
recognitionsequence.
•Neoschizomersarerestrictionenzymesthatrecognizethesame
nucleotidesequenceastheirprototypebutcleaveatadifferentsite.