Biological database
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The document discusses various types of biological databases. It describes primary databases that contain original data, secondary databases that contain processed data derived from primary databases, and composite databases that collect and filter data from multiple primary databases. Examples of specific biological databases are provided, including nucleic acid databases like GenBank, protein sequence databases like Swiss-Prot, protein structure database PDB, and metabolic pathway database KEGG. Details about the purpose and features of some of these major databases like GenBank, DDBJ, EMBL, Swiss-Prot, and PDB are outlined in the document.
Biological database
- 1. BIOLOGICAL DATABASE Dr. Nusaifa Beevi.P Associate Professor & HOD, PG Department of Botany, Iqbal College, Peringammala
- 2. BIOLOGICAL DATABASES Collection of files containing records of biological data in machine readable form Can be accessed, added, retrieved, manipulated and modified Store, manage, connect and distribute data Data are arranged by sets of rules which are programmed into software that manages the data called Database Management System or DBMS.
- 3. Primary Databases: Contain original data in the form of primary sequence data or structural data as submitted by the scientific community. Secondary Databases: Contain information that has been processed and derived from the raw data available in primary database.eg: PROSITE, PRINTS, BLOCKS etc.. Composite Databases: Collect and present data after comparing and filtering them from different primary databases and exhibit only the non- redundant sequences
- 4. Nucleic acid databases: Gen Bank, EMBL,DDBJ Protein sequence databases: PIR, Swiss-Prot, UNIPROT Protein structure database: PDB Metabolic databases: KEGG
- 5. Composed of a group of nucleotide sequence entries. Data repositories that accept nucleic acid sequence data and make it freely available to the public. GenBank, EMBL,DDBJ are principal nucleotide databases. All the three are members of the International Nucleotide Sequence Database Consortium (INSDC) and interchange data.
- 6. Hosted by National Centre for Biotechnology Information (NCBI), situated at the campus of US National Institute of Health, USA. Gen Bank offers all publicly available nucleotide sequences, their protein translation, and their annotated information. It also facilitate direct submission of sequence data by a user friendly process. Researchers from anywhere can submit their data to Gen Bank. An accession number is given to the submitted sequence and then released to the public database after the quality assurance check. This information can be retrieved using the Entrez retrieval system. We can access the data in NCBI over the internet through their site, http://www.ncbi.nlm.nih.gov/genbank
- 8. Started in 1986, hosted now at National Institute of Genetics, Japan. Gather data mainly from scientists in Japan and from researchers all over the world. This can also share nucleotide sequence data with Gen Bank and EMBL. About 99% of the nucleotide data in INSDC submitted by Japanese researchers through DDBJ, and enhances the quality of INSDC. It includes details of sequences, submitters details, biological significance , and the scientific name and taxonomy of the organism. In addition, features that identify coding region, transcription units, mutation sites etc. are also displayed in a feature table.
- 9. Major activities of the DDBJ include, providing internationally recognized accession numbers to sequences, bioinformatics database management, developing tools for the analysis and visualization of biological data, and also conducting courses for beginners to reduce the complexity in the biological data analysis. DDBJ can be accessed through homepage, http://www.ddbj.nig.ac.jp/.
- 11. European Molecular Biology Laboratory Nucleotide Sequence Database, first established in 1974. Hosted at UK by the EMBL European Bioinformatics Institute. EMBL is a non-profit research institution supported by 20 European countries and Australia, for Molecular Biology Research. EMBL collects nucleotide sequence data from individual researchers, genome sequence projects and patent applications. Sequences are stored in this database as they would exist in the biological state. The stored data correspond to wild type sequences without mutation or genetic manipulation. Accessed through the URL, http://www.ebi.ac.uk/embl
- 13. An array of amino acid sequence entries arranged according to the identification number. Well known protein sequence databases available on www are ◦ Swiss-Prot ◦ PIR ◦ UNIPROT
- 14. Developed by the Swiss Institute of Bioinformatics (SIB) and European Bioinformatics Institute(EBI). High quality, manually annotated protein sequence database created in 1986. It provides high level annotations with functions of protein and post transcriptional modifications. It provide all known relevant information about a particular protein. Consists of two sections:- UniProt KB/Swiss-Prot, which is manually annotated and is reviewed, and Uni ProtKB/TrEMBL, which is automatically annotated and not reviewed. Available at http://www.expasy.ch/sprot
- 16. Protein Information Resource database Established in 1984, by National Biomedical Research Foundation (NBRF). It is an integrated public bioinformatics resource that support genomic and proteomic research, and scientific studies. It assists researchers in the identification and interpretation of protein sequence information. PIR can be searched for entries or sequence similarity searches. Can be downloaded at http://www.pir.georgetown.edu/. PIR offers a variety of resources mainly oriented to assist the propagation and standardization of protein annotation.
- 18. It provide a comprehensive, high quality and freely accessible resource of protein sequence. Entries are derived from genome sequencing projects. The Uniprot consortium comprises the European Bioinformatics Institute(EBI),the Swiss Institute of Bioinformatics(SIB), And the Protein Information Resourse(PIR). Uniprot is composed of four components, each optimized for different uses.
- 19. 1. UniProt Knowledge Base (UniProtKB)- For extensive curated protein information with two sections-UniProt KB/Swiss-Prot, which is manually annotated and is reviewed, and Uni ProtKB/TrEMBL, which is automatically annotated and not reviewed. 2. UniProt Reference Clusters (UniRef) 3. UniProt Archive (UniParc) 4. UniProt Metagenomic and Environmental Sequences (UniMes)
- 21. Many proteins which exhibit a common evolutionary origin, show structural similarities. Dissimilar proteins exhibit changes in primary, secondary, teritiary and quarternary structures. Similar or dissimilar protein structure can be predicted with structure database. These databases store a collection of three dimensional structures of proteins.
- 22. Understanding the shape of a molecule helps to understand how it works. PDB is the main primary database used for the prediction of 3D Structures of proteins and nucleic acids. The single world wide archive of structural data. Maintained by the Research Collaboratory for structural bioinformatics (RCSB) The data obtained from X-ray chrystallography and NMR-spectroscopy, are submitted to the PDB. Then, these structures are annotated as per the depositors specifications. Freely available and accessed through URL http://www.pdb.org/
- 24. MODs are also called Organism – specific databases. They describe genome and other information about well studied experimental organisms in life sciences. They store large volumes of data and allow users to analyse results and interpret datasets and data they generated. ( organism of their own interest). Examples: Fly Base- database of Drosophilla melanogaster SGD- Sacharomyces Genome Database AGR- Arabidopsis Genome Resource HGP- Human Genome Project RGD- Rat Genome Database etc…
- 25. Provide information on the biodiversity of a particular area or group of living organisms. They may store genus level information, species level information, information on nomenclature or any combination of the three. Species 2000 ◦ Established in September 1994, by the International Union of Biological Sciences(IUBS), in co-operation with the committee on Data for science and technology(CODATA) and the International Union of Microbiological Sciences(IUMS). ◦ It is a Federation of database organizations working closely with users, taxonomists and sponsoring agencies. ◦ It plans to create an array of participant global species databases covering each of the major groups of organisms(plants, animals, fungi and microbes) ◦ The goal of species 2000 is to provide a uniform and validated quality index of names of all known species for use as a practical tool.
- 26. Thank You