Bioinformatics introduction
- 1. BIOINFORMATICS Name: Anuja Vilas Konde Msc II
- 2. CONTENT What is bioinformatics ? What is data and information? Biological databases Types of biological databases Retrieval of databases Advantages of biological databases
- 3. Bioinformatics Definition Marriage between computer science and Molecular Biology. Techniques of computer science problems of molecular biology. Information technology applied to analyse biological data. Helps to gain understanding of biological data. Plays important role in molecular medicine, evolutionary studies, drug development and in biotechnology. Analysis of gene and protein expression, comparison of genomic data , storing of biological information.
- 4. Data and Information Raw data Processed and Analysed Information
- 5. BIOLOGICAL DATABASES Biological Living. Databases Collection of data in organized manner (i.e information ) Libraries of life sciences information, collected from scientific experiments which is stored using computational analysis. Information Accessed, Managed and updated. Features: Data heterogeneity High volume data Data curation
- 6. Types of biological databases Biological databases Primary Secondary Basis on source of data: Basis of databases stored: Biological databases Sequence Nucleic acid Protein Structure PDB SCOP CATH
- 7. On The basis of Data sources Primary databases : Contains experimentally derived data i.e raw data Examples: Nucleotide sequence, Protein or Macromolecular sequence Experimental results submitted into databases . Swiss Prot, PIR , Gen bank, DDBJ. Secondary databases : Data derived from analysing primary data i.e information Examples: Conserved regions, Signature sequence etc Submitted data Analysed and stored SCOP, CATH
- 8. On basis of data stored Structural databases : Includes structures of experimentally derived proteins and domains Main aim is to organize protein structure providing biological community to access the information A. PDB ( Protein Data Bank): Databases of experimentally determined 3D structure of protein Currently stores 80,000 protein structure Obtained from NMR spectroscopy and X ray crystallography Easily accessible, can be downloaded and utilised
- 9. B. SCOP (Structural classification of proteins): Contains information about classification and structures of proteins Also describes evolutionary relation between proteins. Currently contains 38,000 protein structures Freely accessible to the internet C. CATH ( Class architecture topology homology): Contains information about classification and structures of proteins. also gives information of bonding of proteins and evolutionary relationships of proteins. currently contains 8,078 proteins domains information
- 10. Sequence databases : Composed of large collections of nucleic acid sequence, protein sequence stored in computer. Mainly of two types Nucleic acid sequence: Contains collections of sequences of genome, gene and transcript sequence. Three chief databases store and make available raw nucleic acid data to public Gene bank, EMBL, and DDBJ referred to as primary sequence databases. Genebank: Located in USA. Accessible through NCBI portal Contains annotated collections of nucleotide sequence and their protein translations. Receives 100,000 distinct organism sequences from all over world.
- 11. EMBL( European molecular biology laboratory): Maintained by EBI (European bioinformatics Institute) Comprises of primary nucleotide sequence Data receives from genome sequencing centers. DDBJ (DNA data bank of Japan) : 1. Located at the National Institute of Genetics (NIG). 2. Only nucleotide sequence data bank in Asia. 3. Exchange data with Gen Bank and EMBL. 4. Mainly receives data from Japanese researchers.
- 12. Protein sequence : 1. Database which include a protein’s amino acid sequence, conformation, structure, and features such as active sites. 2. Compiled by the translation of DNA sequences from different gene databases. 3. Important resource because proteins mediate most biological functions. 4. Includes PIR, Swiss PROT, PDB. 1.PIR (Protein Information Resource): 2. Established in 1984 by National Biomedical Research Foundation 3. Provides a high level of annotation. 4. Contains sequence of amino acid and information about protein function prediction 5. Also contains sequences of domains.
- 13. Swiss PROT: 1. Swiss institute of bioinformatics in collaborations with EMBL data provides a databank 2. very high quality and consistent annotations 3. It incorporates: Functions of proteins A. Post-translational modification such as phosphorylation, acetylation B. domains and sites C. Secondary structural feature and quaternary structure of the protein. PDB (Protein data bank) : 1. Includes sequences of proteins. 2. Helps to predict 3D structure of proteins. 3. Database holds data derived from mainly two sources: Structure determined by X-ray crystallography, NMR experiments
- 14. Retrieval of biological databases Accessing the stored data of an organism or a particular gene from the databases. When obtaining a new DNA sequence, one needs to know whether it has already been deposited in the databanks. Requirement for retrieval: name of organism name of gene Data retrieval system : Entrez SRS BLAST
- 15. Entrez : Molecular biology databases and retrieval system Developed by NCBI Nucleotide and protein sequence data, 3D structure data Easy to access but limited information to search SRS ( Sequence retrieval system) Home to over 80,000 biological databases Developed by European Bioinformatics Institute (EBI) Includes sequence of metabolic pathways, transcription factors, and conserved regions. Provides the description of gene, date on which it is uploaded and updated.
- 16. BLAST (Basic Local Alignment Search Tool) : Developed by NCBI Blast programs were designed for fast database searching. Helps to retrieve the data Also helps for comparing primary biological sequence information Raw data obtained from experiment Submit that data to databases Accession number Entry accession number in blast Search Find relationship among them
- 17. Variants of BLAST BLASTN - Compares a DNA query to DNA databases BLASTP - Compares a protein query to a protein database. BLASTX - Compares a DNA query to a protein database , by translating the query in the 6 possible frames . TBLASTN -Compares a protein query to a DNA database, in the 6 possible frames of the database.
- 18. Advantages Databases act as a store house of information. Used to store and organize data in such a way that information can be retrieved easily via a variety of search criteria. It allows knowledge discovery, which refers to the identification of connections between pieces of information . Databases are important tools in assisting scientists to analyze and explain a host of biological phenomena from the structure of biomolecules and their interaction, to the whole metabolism of organisms and to understanding the evolution of species.
- 19. THANK YOU