Bioinformatics issues and challanges presentation at s p college
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This document provides an overview of bioinformatics and some key concepts: - It discusses the exponential growth of biological data from technologies like PCR and microarrays, and how bioinformatics is needed to analyze this data. - Bioinformatics is defined as integrating biology and computer science to collect, analyze, and interpret large amounts of molecular-level information. It uses databases and tools to study genomes, proteins, and biological processes. - Major databases like GenBank, EMBL, and SwissProt store DNA, RNA, protein sequences and provide access to researchers. Tools like BLAST are used to search databases and analyze sequences. - Benefits of bioinformatics include advances in medicine, agriculture, forensics
Bioinformatics issues and challanges presentation at s p college
- 1. Dr N A Ganai Professor Centre of Animal Biotechnology SKUAST-Kashmir
- 2. Contents Introduction to Bioinformatics Complexity of life Size of genome Exponential growth in information generation Why and how to handle this information Definition of Bioinformatics? Data bases Tools Scope of Bioinformatics Anticipated benefits Ethical, Legal, and Social Issues
- 4. DNA is not merely a molecule with a pattern; it is a code, a language, and an information storage mechanism
- 5. Size of Human Genome Each cell carries: 3.2 billion base pairs A code you need to write in 500 books, each book of 500 pages Length of DNA in adult man: The total length of DNA present in one adult human is calculated as: (length of 1 bp)(number of bp per cell)(number of cells in the body) (0.34 × 10-9 m)(6 × 109)(1013) 2.0 × 1013 meters That is the equivalent of nearly 70 trips from the earth to the sun and back.
- 7. Human Genome Project • HGP: International research effort • Began 1990, completed 2003 • Biggest ever project in life sciences • 20 labs participated world around • Next steps for ~30,000 genes – Function and regulation of all genes – Significance of variations between people – Cures, therapies, “genomic healthcare”
- 9. From DNA to Cell Function DNA sequence (split into genes) Amino Acid Sequence Protein 3D Structure Protein Function Cell Activity codes for folds into dictates determines has Lecture 2
- 11. Year Base Pairs Sequences 1982 680,338 606 1983 2,274,029 2,427 1984 3,368,765 4,175 1985 5,204,420 5,700 1986 9,615,371 9,978 1987 15,514,776 14,584 1988 23,800,000 20,579 1989 34,762,585 28,791 1990 49,179,285 39,533 1991 71,947,426 55,627 1992 101,008,486 78,608 1993 157,152,442 143,492 1994 217,102,462 215,273 1995 384,939,485 555,694 1996 651,972,984 1,021,211 1997 1,160,300,687 1,765,847 1998 2,008,761,784 2,837,897 1999 3,841,163,011 4,864,570 2000 11,101,066,288 10,106,023 2001 15,849,921,438 14,976,310 2002 28,507,990,166 22,318,883 2003 36,553,368,485 30,968,418 2004 44,575,745,176 40,604,319 2005 56,037,734,462 52,016,762 2006 69,019,290,705 64,893,747 2007 83,874,179,730 80,388,382 2008 99,116,431,942 98,868,465 Av. Growth in data generation : 5400 times per year
- 13. Exponential Growth in Biological Databases: High throughput Technologies PCR : by Kary Mullis 1983 - an employee of Cetus Corporation, a biotechnology firm in California Awarded the Nobel Prize for the discovery of PCR in 1993
- 14. Microarray Technology Real-Time PCR DNA Chips
- 15. Sequencing Sanger method : 1975 Chain Termination Method Maxam Gilbert : 1977 Chemical Modification Method Next Generation: 1994 High Throughput Parallel sequencing Entire genome can be sequenced in a matter of weeks
- 16. History of DNA Sequencing Avery: Proposes DNA as ‘Genetic Material’ Watson & Crick: Double Helix Structure of DNA Holley: Sequences Yeast tRNAAla 1870 1953 1940 1965 1970 1977 1980 1990 2002 Miescher: Discovers DNA Wu: Sequences Cohesive End DNA Sanger: Dideoxy Chain Termination Gilbert: Chemical Degradation Messing: M13 Cloning Hood et al.: Partial Automation • Cycle Sequencing • Improved Sequencing Enzymes • Improved Fluorescent Detection Schemes 1986 • Next Generation Sequencing •Improved enzymes and chemistry •Improved image processing Adapted from Eric Green, NIH; Adapted from Messing & Llaca, PNAS (1998) 1 15 150 50,000 25,000 1,500 200,000 50,000,000 Efficiency (bp/person/year) 15,000 100,000,000,000 2008
- 17. The Genome Sequence is at hand…so? “The good news is that we have the human genome. The bad news is it’s just a parts list”
- 18. • Gene number, exact locations, and functions • Gene regulation • DNA sequence organization • Noncoding DNA types, amount, distribution, information content, and functions • Coordination of gene expression, protein synthesis, and post-translational events • Interaction of proteins in complex molecular machines • Predicted vs experimentally determined gene function • Evolutionary conservation among organisms • Protein conservation (structure and function) • Proteomes (total protein content and function) in organisms • Correlation of SNPs (single-base DNA variations among individuals) with health and disease • Disease-susceptibility prediction based on gene sequence variation • Genes involved in complex traits and multigene diseases • Complex systems biology including microbial consortia useful for environmental restoration • Developmental genetics, genomics What Next??? We need to know every part, its function and application
- 19. What is Bioinformatics? The newest, fastest growing specialty in the life sciences that integrates biotechnology and computer science. Computers aid to collect, analyze, and interpret biological information at the molecular level. Bioinformatics encompasses a set of software tools that aid in: molecular sequence analysis, structural analysis functional analysis of genes & genomes and their corresponding products
- 20. Understand a living cell and how it functions at molecular level Develop data basses and computational tools Tools are used to mine (analyze) databases to generate knowledge to better understand the living systems Goal of Bioinformatics
- 21. Biological Data basses : Why Why? Store all the data (information) related to Genomics, Transcriptomics, preoteomics, Metabolomics in Data Bases Make biological data available to scientists. To make biological data available in computer-readable form. Types of Databases Primary Databases: Store raw DNA/RNA and protein data submitted by scientists GenBank: by NCBI USA www.ncbi.nlm.nih.gov/genbank/ EMBL: European : www.ebi.ac.uk/embl/ DDBJ: Japan www.ddbj.nig.ac.jp/ PDB: Protein Data bank http://www.rcsb.org/pdb/home/home.do
- 22. Data Bases … cont. Secondary data bases: Contain computationally processed or manually curetted information based on primary data bases. SWISS-Prot: Curetted protein data base www.ebi.ac.uk/swissprot TrEMBL: Translated Nucleic acid sequences in EMBL PIR: annotated protein sequences UniProt: Combined database of SWISSProt, TrEMBL, PIR Prosite PRINTS BLOCKS PFAM Specialized Data bases :cater to a particular research interest FlyBase HIV Sequence data base Ribosome data base OMIM Microarray Gene expression database ExPASY etc. etc.
- 23. We need Bioinformatics Tools… To mine (analyze) databases to generate knowledge to better understand the living systems Search/compare databases Sequence Analysis Genomics Phylogenics Structure Prediction Molecular Modelling Microarrays Packages, Misc Apps, Graphics, Scripts
- 24. Examples of Bioinformatics Tools Database interfaces (Search Tools) Genbank/EMBL/DDBJ, Medline, SwissProt, PDB, … Sequence alignment BLAST, FASTA (Fast All) Multiple sequence alignment Clustal, MultAlin, DiAlign Gene finding Genscan, GenomeScan, GeneMark, GRAIL Protein Domain analysis and identification pfam, BLOCKS, ProDom, Pattern Identification/Characterization Gibbs Sampler, AlignACE, MEME Protein Folding prediction PredictProtein, SwissModeler
- 25. Five websites that all biologists should Bookmark NCBI (The National Center for Biotechnology Information; http://www.ncbi.nlm.nih.gov/ EBI (The European Bioinformatics Institute) http://www.ebi.ac.uk/ The Canadian Bioinformatics Resource http://www.cbr.nrc.ca/ SwissProt/ExPASy (Swiss Bioinformatics Resource) http://expasy.cbr.nrc.ca/sprot/ PDB (The Protein Databank) http://www.rcsb.org/PDB/
- 26. Anticipated Benefits of Genome Research & Bioinformatics Molecular Medicine : Gene Testing , Pharmacogenomics Gene Therapy improve diagnosis of disease detect genetic predispositions to disease create drugs based on molecular information use gene therapy and control systems as drugs design “custom drugs” (pharmacogenomics) based on individual genetic profiles Microbial Genomics rapidly detect and treat pathogens in clinical practice develop new energy sources (biofuels) monitor environments to detect pollutants protect citizenry from biological and chemical warfare clean up toxic waste safely and efficiently
- 27. DNA Identification (Forensics) identify potential suspects whose DNA may match evidence left at crime scenes exonerate persons wrongly accused of crimes establish paternity and other family relationships identify endangered and protected species as an aid to wildlife officials (could be detect bacteria and other organisms that may pollute air, water, soil, and food match organ donors with recipients in transplant programs determine pedigree for seed or livestock breeds Benefits: …contined
- 28. Agriculture, Livestock Breeding, and Bioprocessing grow disease-, insect-, and drought-resistant crops breed healthier, more productive, disease-resistant farm animals grow more nutritious produce develop biopesticides incorporate edible vaccines incorporated into food products develop new environmental cleanup uses for plants like tobacco Benefits …cont .
- 29. ELSI: Ethical, Legal, and Social Issues • Privacy and confidentiality of genetic information. • Fairness in the use of genetic information by insurers, employers, courts, schools, adoption agencies, and the military, among others. • Psychological impact, stigmatization, and discrimination due to an individual’s genetic differences. • Reproductive issues including adequate and informed consent and use of genetic information in reproductive decision making. • Clinical issues including the education of doctors and other health- service providers, people identified with genetic conditions, and the general public about capabilities, limitations, and social risks; and implementation of standards and quality-control measures. Health and environmental issues concerning genetically modified foods (GM) and microbes. Commercialization of products including property rights (patents, copyrights, and trade secrets) and accessibility of data and materials.
- 30. Common Questions of a Student of biology