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databases in bioinformatics
This document discusses databases in bioinformatics. It begins by noting the rapid increase in biological data from sources like gene sequences, protein sequences, structural data, and gene expression data. It then defines biological databases as structured, searchable collections of data that are periodically updated and cross-referenced. The major purposes of databases are to make biological data available, systematize the data, and allow analysis of computed biological data. The document provides a brief history of biological databases and sequencing efforts. It also classifies biological databases based on data type, maintenance status, data access, data sources, database design, and organism. Specific databases discussed include DDBJ, EMBL, GenBank, Swiss-Prot, and NCB
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An introduction to the significance of databases in bioinformatics, with emphasis on various biological data types including gene sequences and protein structures.
Definition of biological databases, their functionalities, and a brief history of database development from the first sequence databases to the era of genomic information.
Highlights the progression of genomic research including the concept and importance of genome sequencing and methodologies for gene prediction.
Details the characteristics of biological databases, their classification schemes, and the various types of biological databases based on specific criteria.
Describes the status of database maintenance and categories of data access including public, proprietary, and restricted databases.
Explains the distinction between primary databases, which hold original research data, and secondary databases that compile data from primary sources.
Insight into collaborations between major databases like DDBJ and SWISS-PROT, focusing on their roles in nucleotide and protein sequence storage.
Wrap-up of the presentation with well wishes to the audience.
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databases in bioinformatics
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- 2. Introduction Fast increasein biological information Biological science has now turned into a data rich science Gene sequences Amino acid sequences in proteins Motifs and domains in proteins Structural data from XRD & NMR Metabolic pathways Protein-protein interactions Gene expression data DNA microarrays
- 3. Biological databases Biologicaldatabase is a collection of data which is structured, searchable, updated periodically and also cross- referenced. Some databases are multi functional Major purposes of databases is as follows:Availability of biological data Systemization of data Analysis of computed biological data
- 4. History 1956; firstsequence database when insulin was sequenced 51 amino acids Atlas of protein sequences and structures in 1965 by Margaret Day Hoff et al was a printed book. Became base for PIR protein information resource First nucleotide sequence: yeast tRNA 77 bases During this time 3D structure of proteins was being studied and renowned PDB was made.
- 5. … First genomepublished was of free living virus haemophilus influenzae in 1995 Genome? All genes ? Or all DNA? Why are complete genome interesting?
- 6. Aspects of genomeanalysis Ab initio Gene prediction Locus Gene identification by EST (expressed sequence tags) Gene prediction via EST Gene prediction via comparison, coding and regulatory regions
- 7. Features of biological databases 1)Data heterogeneity 2) High volume data 3) Uncertainty 4) Data Curation 5) Large scale data integration 6) Data sharing 7) Dynamic and subject to change
- 8. Classification scheme for biologicaldatabases Data type Maintenance status Data access Data source Database design Organism
- 9. Data type Genomedatabase Sequence database Structure database Microarray database Chemical database Pathway database Enzyme database Disease database Literature database
- 10. Based on maintenancestatus NCBI EMBL SIB
- 11. Based on dataaccess 1) Publicly available 2) Available with copy wright 3) Browsing only, accessible but not downloadable 4) Academic but not freely available 5) Proprietary commercial 6) Restricted
- 12. Based on datasources Based on data sources
- 13. Primary databases Containsoriginal data from the researchers Public or open access mostly NCBI , GENEBANK EMBL SWISS-PROT NDB
- 14. Secondary databases Resultsfrom entries of primary database Manually created or automatically generated Swiss-prot is an example of secondary database
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- 17. DDBJ DNA databankof japan Nucleotide sequence database Established in 1986 Has been working in collaboration with EMBL & NCBI After 20 years another collaborative project named INSDC was formed EMBL Genebank DDBJ
- 21. SWISS-PROT Protein sequencedatabase Maintained by SIB Swiss institute of bioinformatics in Switzerland and also the European bioinformatics institute EBI The output format is swiss-prot file That has been explained in molecular file formats
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