Bioinformatics

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Bioinformatics

  1. 1. BIOINFORMATICS INSTITUTE OF INDIA BIOINFORMATICS……….AT A GLANCE By :-Mr. Arvind Singh M. Sc Bioinformatics Faculty BII
  2. 2. BIOINFORMATICS INSTITUTE OF INDIA Part I-Introduction to Bioinformatics Part II-Historical Overview of Bioinformatics Part III-Human Genome Project Part IV-Biological Databases Part V-Internet and Bioinformatics Part VI-Knowledge Discovery and Data mining Part VII-Career Prospect In Bioinformatics
  3. 3. BIOINFORMATICS INSTITUTE OF INDIA Part I-Introduction to Bioinformatics
  4. 4. BIOINFORMATICS INSTITUTE OF INDIA Definition of Bioinformatics General Definition: A computational approach ,Solves the biological problem. Bioinformatics is emerging and advance branch of biological science , contain Biology mathematics and Computer Science. Bioinformatics developed a new thought , to maintain the concepts and store .The huge amount of Biological data. Bioinformatics concepts and Method are different than the Biological concepts and method. Bioinformatics, A logical and technical means by which not only solve the Biological problems but also can predicts the new aspects.
  5. 5. BIOINFORMATICS INSTITUTE OF INDIA BIOINFORMATICS ProteomicsGenomics Computational Biology Database Base Management System Systematic Biology Biostatistics Cheminformatics Computational Languages CC++PerlBioperlBiojava Bioinformatics Areas
  6. 6. BIOINFORMATICS INSTITUTE OF INDIA Insilico Areas of Bioinformatics Computational Biology Docking Approaches& New Drug Discovery Protein structure prediction Micro array analysis Comparative Homology Modeling Phylogenetic Analysis Protein Folding Problem
  7. 7. BIOINFORMATICS INSTITUTE OF INDIA Part II-Historical Overview of Bioinformatics
  8. 8. BIOINFORMATICS INSTITUTE OF INDIA HISTORY AND SCOPE OF BIOINFORMATICS • 1859 – The “On the Origin of Species”, published by Charles Darwin that introduced theory of genetic evolution – allows adaptation over time to produce organisms best suited to the environment. • 1869 - The DNA from nuclei of white blood cells was first isolated by Friedrich Meischer. • 1951 – Linus Pauling and Corey propose the structure for the alpha- helix and beta-sheet. • 1953 - Watson and Crick propose the double helix model for DNA based on x-ray data obtained by Franklin and Wilkins. • 1955 - The sequence of the first protein to be analyzed, bovine insulin, is announced by F. Sanger. • 1958 - The Advanced Research Projects Agency (ARPA) is formed in the US. •
  9. 9. BIOINFORMATICS INSTITUTE OF INDIA • 1973 - The Brookhaven Protein Data Bank(PDB) is announced. • 1987 - Perl (Practical Extraction Report Language) is released by Larry Wall. •10. 1988 - National Centre for Biotechnology Information (NCBI) founded at NIH/NLM. •11. 1990 - Human Genome Project launched •BLAST program introduced by S. Karlin and S.F. Altshul. • Tim Berners-Lee, a British scientist invented the World Wide Web in 1990. •12. 1992 - The Institute for Genome Research (TIGR), associated with plans to exploit sequencing •commercially through gene identification and drug discovery, was formed. •13. 2001 - The human genome (3,000 Mbp) is published. HISTORY AND SCOPE OF BIOINFORMATICS
  10. 10. BIOINFORMATICS INSTITUTE OF INDIA Future Goals Of Molecular Biology and Bioinformatics Research 2010 :Completion of the 2010 Project: to understand the function of all genes within their cellular, organism and evolutionary context of Arabidopsis thaliana. 2050: To complete of the first computational model of a complete cell, or maybe even already of a complete organism.
  11. 11. BIOINFORMATICS INSTITUTE OF INDIA Part III-Human Genome Project Part III-Human Genome Project
  12. 12. BIOINFORMATICS INSTITUTE OF INDIA Human Genome Project U.S. govt. project coordinated by the Department of Energy and the National Institutes of Health, launched in 1986 by Charles DeLisi. Definition: GENOME – the whole hereditary information of an organism that is encoded in the DNA. Aims of the project: To identify the approximate 100,000 genes in the human DNA. Determine the sequences of the 3 billion bases that make up human DNA. Store this information in databases. Develop tools for data analysis. Address the ethical, legal, and social issues that arise from genome research.
  13. 13. BIOINFORMATICS INSTITUTE OF INDIA Whose genome is being sequenced? A group of researchers have managed to complete a genetic map of the bacterium Haemophilus influenzae The approach called whole Genome Shotgun Sequencing to sequence the 1,749 genes of the bacterium in minimum time period. The H. influenzae project was based on an approach to genomic analysis using sequencing and assembly of unselected pieces of DNA from the whole chromosome
  14. 14. BIOINFORMATICS INSTITUTE OF INDIA Benefits of Human Genome Project research Improvements in medicine and Drugs used in genetic or metabolic disorder. Microbial genome research for Bio-fuel and environmental cleanup. DNA finger printing & forensics. Improved agriculture by improving the wild gene of high yielding variety of grain and livestock. Better understanding of species evolution and Human genome . More accurate risk assessment by gene mapping.
  15. 15. BIOINFORMATICS INSTITUTE OF INDIA Part IV-Internet and BioinformaticsPart IV-Internet and Bioinformatics
  16. 16. BIOINFORMATICS INSTITUTE OF INDIA Internet and Bioinformatics Internet plays an important role to retrieve the biological information. Bioinformatics emerging new dimension of Biological science, include The computer science ,mathematics and life science. The Computational part of bioinformatics use to optimize the biological problems like (metabolic disorder, genetic disorders). Computational part contains: Computer Science Operating System Win 2000XPLinuxUnix Database Development Software & Tools Development Software & Tools Application
  17. 17. BIOINFORMATICS INSTITUTE OF INDIA Internet and Bioinformatics The Mathematical portion helps to understand the algorithms used in Bioinformatics software and tools. The mathematical portion which, used in Bioinformatics are : Mathematics Biostatistics (HMM, ANN in secondary structure prediction) DiffrentiationIntigration (Time and space complexity E-value ,p-values in Blast) Complex Mathematics Functions (Fourier Transformation) Matrices (Sequence alignment, Blast Fast, MSA & Phylogenetic Prediction)
  18. 18. BIOINFORMATICS INSTITUTE OF INDIA Internet and Bioinformatics The Internet is a global data communications system. It is a hardware and software infrastructure that provides connectivity between computers. The Web is one of the services communicated via the Internet. It is a collection of interconnected documents and other resources, linked by hyperlink and URLs.
  19. 19. BIOINFORMATICS INSTITUTE OF INDIA Graph of internet users per 100 inhabitants between 1997 and 2007
  20. 20. BIOINFORMATICS INSTITUTE OF INDIA Internet Resources for Bioinformatics Database Search Engine NCBISwiss-Prot Uni-Prot-K Online serve tools Clustal WSwiss-Model Serve Biological Databases PrimarySecondaryComposite Bioinformatics Software’s Development Online Databases KEGG ModBasePDBZinc DatabaseMolSoft Bioinformatics Software’s Application Relational Database Management System Other Software & Information Sources
  21. 21. BIOINFORMATICS INSTITUTE OF INDIA Part V- Biological Databases Part V- Biological Databases
  22. 22. BIOINFORMATICS INSTITUTE OF INDIA Biological Databases Type of databases Information Contain Bibliographic databases Literature Taxonomic databases Classification Nucleic acid databases DNA information Genomic databases Gene level information Protein databases Protein information Protein families, domains and functional sites Classification of proteins and identifying domains Enzymes/ metabolic pathways Metabolic pathways
  23. 23. BIOINFORMATICS INSTITUTE OF INDIA Types Of Biological Databases Accessible There are many different types of database but for routine sequence analysis, the following are initially the most important. Primary databases Secondary databases Composite databases Primary Database (Nucleic AcidProtein) EMBL Genbank DDBJ SWISS-PROT TREMBL PIR
  24. 24. BIOINFORMATICS INSTITUTE OF INDIA Secondary databases PROSITE Pfam BLOCKS PRINTS Secondary databases
  25. 25. BIOINFORMATICS INSTITUTE OF INDIA Composite databases Combine different sources of primary databases. Composite database's NRDB OWL
  26. 26. BIOINFORMATICS INSTITUTE OF INDIA The International Sequence Database Collaboration EMBL GenBank DDBJ
  27. 27. BIOINFORMATICS INSTITUTE OF INDIA GenBank GenBank® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences DDBJ DDBJ (DNA Data Bank of Japan) began DNA data bank activities in earnest in 1986 at the National Institute of Genetics (NIG) with the endorsement of the Ministry of Education, Science, Sport and Culture. The Center for Information Biology at NIG was reorganized as the Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ) in 2001. The new center is to play a major role in carrying out research in information biology and to run DDBJ operation in the world.
  28. 28. BIOINFORMATICS INSTITUTE OF INDIA EMBL Nucleotide Sequence Database The EMBL Nucleotide Sequence Database (also known as EMBL-Bank) constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications. The database is produced in an international collaboration with GenBank (USA) and the DNA Database of Japan (DDBJ).
  29. 29. BIOINFORMATICS INSTITUTE OF INDIA Part VI-Knowledge Discovery and Data minigPart VI-Knowledge Discovery and Data mining
  30. 30. BIOINFORMATICS INSTITUTE OF INDIA Why Data Mining ? Biology: Language and Goals A gene can be defined as a region of DNA. A genome is one haploid set of chromosomes with the genes they contain. Perform competent comparison of gene sequences across species and account for inherently noisy biological sequences due to random variability amplified by evolution Assumption: if a gene has high similarity to another gene then they perform the same function Analysis: Language and Goals Feature is an extractable attribute or measurement (e.g., gene expression, location) Pattern recognition is trying to characterize data pattern (e.g., similar gene expressions, equidistant gene locations). Data mining is about uncovering patterns, anomalies and statistically significant structures in data (e.g., find two similar gene expressions with confidence > x)
  31. 31. BIOINFORMATICS INSTITUTE OF INDIA What is Data Mining Data mining (knowledge discovery from data) Extraction of interesting (non-trivial, implicit, previously unknown and potentially useful) patterns or knowledge from huge amount of data Data mining: a misnomer? Alternative names Knowledge discovery (mining) in databases (KDD), knowledge extraction, data/pattern analysis, data archeology, data dredging, information harvesting, business intelligence, etc. Watch out: Is everything “data mining”? Simple search and query processing (Deductive) expert systems
  32. 32. BIOINFORMATICS INSTITUTE OF INDIA Evolution of Database Technology 1960s: Data collection, database creation, IMS and network DBMS 1970s: Relational data model, relational DBMS implementation 1980s: RDBMS, advanced data models (extended-relational, OO, deductive, etc.) Application-oriented DBMS (spatial, scientific, engineering, etc.) 1990s: Data mining, data warehousing, multimedia databases, and Web databases 2000s Stream data management and mining Data mining and its applications Web technology (XML, data integration) and global information systems
  33. 33. BIOINFORMATICS INSTITUTE OF INDIA Why Data Mining?—Potential Applications Data analysis and decision support Market analysis and management  Target marketing, customer relationship management (CRM),  market basket analysis, cross selling, market segmentation  Risk analysis and management  Forecasting, customer retention, improved underwriting,  quality control, competitive analysis Fraud detection and detection of unusual patterns (outliers) Other Applications Text mining (news group, email, documents) and Web mining Stream data mining Bioinformatics and bio-data analysis
  34. 34. BIOINFORMATICS INSTITUTE OF INDIA Data Mining Techniques S ta tis tics M a c h in e le a rn in g D a ta b a s e te c h n iq u e s P a tte rn re co g n itio n O p tim iz a tio n te c h n iq u e s D a ta m in in g te c h n iq u e s d ra w fro m
  35. 35. BIOINFORMATICS INSTITUTE OF INDIA Architecture: Typical Data Mining System data cleaning, integration, and selection Database or Data Warehouse Server Data Mining Engine Pattern Evaluation Graphical User Interface Knowl edge- Base Database Data Warehouse World-Wide Web Other Info Repositories
  36. 36. BIOINFORMATICS INSTITUTE OF INDIA – Data mining—core of knowledge discovery process Data Cleaning Data Integration Data Warehouse Task-relevant Data Selection Data Mining Pattern Evaluation Knowledge Discovery (KDD) Process
  37. 37. BIOINFORMATICS INSTITUTE OF INDIA Part VII-Career Prospect In Bioinformatics
  38. 38. BIOINFORMATICS INSTITUTE OF INDIA Develop your carrier …………as SCIENTIST , RESEARCH ASSOCIATE PROF. READER & LECT. IN UNIV COLLEGE TECHNICAL EXCUTIVE IN BUSSINESS & DEV DATA ANALYST IN SCIENTIFIC ORG & LAB BIOSOFT DEVELOPER IN IT INDUSTRY

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