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Primary and secondary database
- 1. PRIMARY AND SECONDARYBIOLOGICAL DATABASE By KAUSHAL KUMAR SAHU Assistant Professor (Ad Hoc) Department of Biotechnology Govt. Digvijay Autonomous P. G. College Raj-Nandgaon ( C. G. )
- 2. CONTANTS • INTRODUCTION • WHATIS DATA AND DATABASE? • WHAT IS BIOLOGICAL DATABASE? • TYPES OF BIOLOGICAL DATABASE – PRIMARY DATABASE • Nucleic acid sequence database • Protein sequence database – SECONDARY DATABASE – COMPOSITE DATABASE – TERTIARY DATABASE • WHY NEED? • CONCLUSION • REFRENCES 5/11/2020 2
- 3. INTRODUCTION Application of computational techniques Management and Analysis ofbiological Data. Bioinformatic History: •The first English use of the word "data" is from the 1640s. • Using the word "data" to mean "transmittable and storable computer information" was first done in 1946. •The first database was created in 1956 . •Insulin protein is the first protein to be sequenced. 5/11/2020 3
- 4. DATA • A seriesof observations, measurements , or facts; information and also called: information computing. DATABASE • A large systematized collecti on of data that can be expanded,updated, and retrieved rapidly for specific purpose. 5/11/2020 4
- 5. BIOLOGICAL DATABASE • Storageof biological information(Nucleic acid sequence, Protein sequence and structure). 5/11/2020 5
- 6. DEFINATION Biological database arecomputer sites that organise, store and disseminate files that contain information consisting of literature references, nucleic acid sequences and Protein sequences and structure. 5/11/2020 6
- 7. SOURCES ON THEWEB FOR IMPORTANT DATABASE 5/11/2020 7
- 8. TYPES OF BIOLOGICALDATABASE 1. • Primary Database 2. • Secondary Database 3. • Composite Database 4. • Tertiary Database 5/11/2020 8
- 9. Primary Database Stores biomolecularsequences (Protein or Nucleic acid ) and associated annotation information (Organism, species, mutation linked to particular diseases, bibliographic etc. ) Primary sources are original materials on which research is based. Neither interpreted nor condensed nor evaluated by other writers. 5/11/2020 9
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- 11. NCBI • Located inBethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper. • Was directed by David Lipman, one of the original authors of the BLAST. • The NCBI houses a series of databases. EX. : GenBank - DNA sequences. PubMed (a bibliographic database ) - the biomedical literature. Other databases - Epigenomics database. 5/11/2020 11
- 12. GenBank • A partof International nucleiotide sequence database collaboration which comprised of EMBL, DDBJ GenBank at NCBI. • The database started in 1982 by Walter Goad and Los Alamos National Laboratory. • In 15 August 2017, GenBank release 221.0 has 203,180,606 loci, 240,343,378,258 bases, from 203,180,606 reported sequences. https://www.revolvy.com/main/index.php?s=GenBank 5/11/2020 12
- 13. EMBL-EBI • Established in1980 at the EMBL laboratories in Heidelberg, Germany. • An international, innovative and interdisciplinary research organisation funded by 23 member states and two associate member states. • Location- Hinxton, Cambridge, UK. 5/11/2020 13
- 14. DDBJ • 1987 DDBJrelease 1 was provided. • Situated in Mishima, Japan. 5/11/2020 14
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- 17. SECONDARY DATABASE • Derivedfrom the analysis of primary data. • Present in the form of regular expressions(patterns), fringerprints, blocks. Secondary databse PROSITE PRINTS 5/11/2020 17
- 18. PROSITE • It isconsists of entries describing the protein families, domains and functional sites as wel as aminocid patterns and profiles in them. • Complemented by collection of rules based profiles and pattern i.e. ProRule. 5/11/2020 18
- 19. PRINTS • Collection ofprotein motif fringerprints. • the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. • Fingerprints can encode protein folds and functionalities more flexibly and powerfully than can single motifs, full diagnostic potency deriving from the mutual context provided by motif neighbours. 5/11/2020 19
- 20. COMPOSITE DATABASE • Representan amalgamation of several primary database sources and are easy to use. • Access all the relevant information from a single source rather than connect to multiple resources. Ex. NCBI, UniProt etc. 5/11/2020 20
- 21. CONCLUSION • Bioinformatics isthe application of information technology to store, organize To make biological data available in computer-readable form. • We can easily analyze the vast amount of biological data which is available in the form of sequences and structures of proteins(the building block of organisms) and nucleic acid (the information carrior). • Need for storing and communicating large datasets has grown . • Make biological data available to scientists. 5/11/2020 21
- 22. REFERENCES • Books: – Bioinformatics– C.S.V.Murthy - edition-1st - 2003 . – Bioinformatics – S.C. Rastogi - edition-1st - 2003. • Other s source: – https://www.ncbi.nlm.nih.gov/nuccore/NC_002371.2 – http://vle.du.ac.in/mod/book/print.php?id=8913&chapterid=12618 – https://web.expasy.org/docs/swiss-prot_guideline.html – nd%20Managing%20Information%20Leicester/page_21.htm – https://bioinf.comav.upv.es/courses/biotech3/theory/databases.ht ml 5/11/2020 22
Editor's Notes
- #4 The first English use of the word "data" is from the 1640s.