GENOMICS AND BIOINFORMATICS

Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble and analyze the function and structure of genomes

1. Genomics and bioinformatics

2. What is genome..? A genome is an organism's complete set of DNA, including all of its genes. Genes carry the information for making all of the proteins required by the body for growth and maintenance. The genome also encodes r-RNA and t-RNA which are involved in protein synthesis .

3. Genomics Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble and analyze the function and structure of genomes (the complete set of DNA within a single cell of an organism). The branch of molecular biology concerned with the structure, function, evolution and mapping of genomes. It involves the study of all genes at the DNA, mRNA and proteome level as well as the cellular or tissue level. The term genomics was first coined in 1986 by Tom Roderick.

4. Contd.., Genomics is the study of the genomes (i.e. the entire hereditary information) of organisms and includes: Determining the entire DNA sequence. Fine-scale genetic mapping. Studies of intragenomic phenomena. Used to determine an ideal genotype instead of just a few genes. The study of whole genomes of populations of individuals can reveal the genetic basis of different responses to both biotic and abiotic stresses. Requires a large amount of information per individual. Expensive in agriculture where many individuals need to be analyzed.

5. history Genomics is a concept that was first developed by Frederick Sanger in early 1970s, who first sequenced the complete genome of a virus and of a mitochondrion. In 1972, Walter Gilbert and his research group became the first to s equence a gene. They sequenced the gene of Bacteriophage MS2. They shared half of the 1980 Nobel prize in chemistry for independently developing methods for the sequencing DNA. In 1995, Hamilton O. Smith and his team became the first to sequence a genome of a free living organism – that of Haemophilus influenzae.

6. Genetics v/s genomics GENETICS Genetics is the study of heredity. “Gene" refers to a specific sequence of DNA on a single chromosome. Genetics involves the study of functions and composition of the single gene. GENOMICS Genomics is the study of the entirety of an organism’s genes. “Genome” refers to an organism's entire genetic makeup. Genomics addresses all genes and their inter relationships.

7. SUB FIELDS OF GENOMICS 1. Structural genomics: Construction of genomic sequence data Gene discovery and localization Construction of gene maps Structural genomics seeks to describe the 3- dimensional structure of every protein encoded by a given genome. 2. Functional genomics: Biological function of genes, Regulation , Products and Plant development studies. Functional genomics focuses on the dynamic aspects such as gene transcription , translation and protein– protein interactions. 3. Comparative genomics: Compares gene sequences to elucidate functional or evolutionary relationships

8. Goals of genomics Sequence the entire genome by cutting it into small, manageable pieces (fragments). Assemble the entire genome from the pieces. Understand how gene expression takes place. Why to sequence the genomes..? Sequencing genomes helps understand how the genome as a whole and how the genes work together to direct the growth, development and maintenance of an entire organism. The genome sequence will represent a valuable shortcut, thus helping to find genes much more easily and quickly.

9. Map-Based Sequencing

10. FINDING THE GENES After sequencing, need to find the genes, using computer algorithms – this step is called ‘annotation’. Annotation identifies : Protein-coding genes Initiation sequences Regulatory sequences Termination sequences Non protein-coding sequences

11. GENE FUNCTION After genome sequencing is annotated, functions need to be assigned to all genes in the sequence. Some of the identified genes might have functions assigned already via classical methods of mutagenesis and linkage mapping. Some may not have assigned functions – use homology searches. Computer-based comparisons of the sequence under study with known sequences from other organisms.

12. GENOMIC DATA Genomic data refers to the genome and DNA data of an organism.

13. Arabidopsis Genome 123

14. BENEFITS OF GENOMICS TO CROP IMPROVEMENT Unlimited possibilities for crop improvement, Especially in combination with genetic engineering: Improved crop productivity Increased nutritional quality and quantity Tolerance to abiotic stresses – drought, low quality soils (acidity, low nutrient content) Tolerance to biotic stresses - pests and diseases Other It can be used in the field of medicine for early detection of genetic diseases and its diagnosis and treatment. To study evolution through mutation lineages. In forensic science.

15. bioinformatics It is an interdisciplinary field that develops methods and software tools for understanding biological data as an interdisciplinary field of science. Bioinformatics combines computer science , statistics , mathematics and engineering to analyze and interpret biological data. It deals with Collection Organization Analysis Manipulation Sharing of Biological Data But at the end of the day it is used to solve the biological problems on molecular level.

16. Bioinformatics in context

17. Central paradigm of bioinformatics Molecular Structure Phenotype (Symptoms) Biochemical Function Genetic Information MVHLTPEEKT AVNALWGKVN VDAVGGEALG RLLVVYPWTQ RFFESFGDLS SPDAVMGNPK VKAHGKKVLG AFSDGLAHLD NLKGTFSQLS ELHCDKLHVD PENFRLLGNV LVCVLARNFG KEFTPQMQAA YQKVVAGVAN ALAHKYH

18. Why bioinformatics is necessary..? The need for bioinformatics has arisen from the recent explosion of publicly available genomic information, such as resulting from the Human Genome Project. Gain a better understanding of gene analysis, taxonomy and evolution. To work efficiently on the rational drug designs and reduce the time taken for the development of drug manually.

19. Goals of bionformatics To uncover the wealth of Biological information hidden in the mass of sequence, structure, literature and biological data. It is being used now and in the fore seeable future in the areas of molecular medicine. It has environmental benefits in identifying waste and clean up bacteria. In agriculture, it can be used to produce high yield low maintenance crops.

20. Field of bioinformatics Molecular Medicine Gene Therapy Drug Development Microbial genome applications Crop Improvement Forensic Analysis of Microbes Biotechnology Evolutionary Studies Bio-Weapon Creation

21. Bioinformatics key areas Organisation of knowledge (Sequences, structures and functional data) homology searches

22. Where bioinformatics works ..? In Experimental Molecular Biology. In Genetics and Genomics. In generating Biological Data. Analysis of gene and protein expression. Comparison of genomic data. Understanding of evolutionary aspect of Evolution. Understanding biological pathways and networks in System Biology. In Simulation & Modeling of DNA, RNA and Protein.

23. How it is useful ? Bioinformatics, being an interface between modern biology and informatics. It involves discovery, development and implementation of computational algorithms and software tools that facilitate an understanding of various biological processes with the goal to serve primarily agriculture and healthcare sectors.

24. The challenge In 1995, the number of genes in the database started to exceed the number of papers on molecular biology and genetics in the literature!

25. Sources of huge Biological Data DNA sequence which determines protein sequence . Protein sequence which determines protein structure . Protein structure which determines protein function Huge data is generated from the above written three sources and now there is need of intelligent storage and analysis of this data so that something useful can be taken out of this data. Therefore, automated computer tools must be developed to allow the extraction of meaningful biological information.

26. Biological Database Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high- throughput experiment technology, and computational analysis. BIOLOGICAL DATABASE INFORMATION THEY CONTAIN Bibliographic database Literature Taxonomic Database Classification Nucleic acid database DNA Information Genomic Database Gene level Information Protein Database Protein Information

27. Bioinformatics in dna sequence databases Three databanks exchange data on a daily basis. Data can be submitted and accessed at either location. DNA Data Bank of Japan ( National Institute of Genetics ) EMBL ( European Bioinformatics Institute ) GenBank ( National Center for Biotechnology Information ) UniProt Universal Pesource ( EBI , Swiss Institute of Bionformatics ) Swiss- Prot Protein Knowledgebase ( Swiss Institute of Bionformatics ) National Center for Biotechnology Information ( NCBI ) NIM,USA

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