BIOINFORMATICS Prepared By : CONTENTS INTRODUCTION WHAT IS BIOINFORMATICS? ORIGIN OF BIOINFORMATICS AIMS OF BIOINFORMATICS NEEDS OF BIOINFORMATICS POTENTIAL OF BIOINFORMATICS LEVELS OF BIOINFORMATICS BIOLOGICAL DATABASE TOOLS OF BIOINFORMATICS IN INDIA APPLICATION PROGRAMMES IN BIOINFORMATICS BIOINFORMATICS PROJECT BIOINFORMATICS AND IT’S SCOPE CONCLUSION INTRODUCTION In the last few decades, advances in molecular biology and the equipment available for research in this field have allowed the increasingly rapid sequencing of large portions of the genomes of several species. In fact, to date, several bacterial genomes, as well as those of some simple eukaryotes (e.g., Saccharomyces cerevisiae, or baker's yeast) have been sequenced in full. The Human Genome Project, designed to sequence all 24 of the human chromosomes, is also progressing. Popular sequence databases, such as GenBank and EMBL, have been growing at exponential rates. This deluge of information has necessitated the careful storage, organization and indexing of sequence information. Information science has been applied to biology to produce the field called Bioinformatics. WHAT IS BIOINFORMATICS? Bioinformatics is the application of computer technology to the management of biological information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied to gene-based drug discovery and development.. The most pressing tasks in bioinformatics involve the analysis of sequence information. Computational Biology is the name given to this process, and it involves the following : Finding the genes in the DNA sequences of various organisms Developing methods to predict the structure and/or function of newly discovered proteins and structural RNA sequences. Clustering protein sequences into families of related sequences and the development of protein models. Aligning similar proteins and generating phylogenetic trees to examine evolutionary relationships. ORIGIN OF BIOINFORMATICS Over a century ago, bioinformatics history started with an Austrian monk named Gregor Mendel. He is known as the "Father of Genetics". He cross-fertilized different colors of the same species of flowers. He kept careful records of the colors of flowers that he cross- fertilized and the color(s) of flowers they produced. Mendel illustrated that the inheritance of traits could be more easily explained if it was controlled by factors passed down from generation to generation. Since mendel, bioinformatics and genetic record keeping have come a long way . AIMS OF BIOINFORMATICS The aims of bioinformatics are basically three-fold. They are Organization of data in such a way that it allows researchers to access existing information & to submit new entries as they are produced. While data-creation is an essential task, the information stored in these databases is useless unless analyzed. Thus the purpose of bioinformatics extends well beyond mere volume control. To develop tools and resources that help in the analysis of data. For example, having sequenced a particular protein, it is with previously characterized sequences. This requires more than just a straightforward database search. As such, programs such as FASTA and PSI-BLAST much consider what constitutes a biologically significant resemblance. Development of such resources extensive knowledge of computational theory, as well as a thorough understanding of biology. Use of these tools to analyze the individual systems in detail, and frequently compared them with few that are related. NEEDS OF BIOINFORMATICS The need for Bioinformatics capabilities has been precipitated by the explosion of publicly available genomic information resulting from the Human Genome Project. The goal of this project - determination of the sequence of the entire human genome (approximately three billion base pairs) - will be reached by the year 2002 Whole Genome Analyses and Sequences. Experimental Analyses involving thousands of Genes simultaneously. DNA Chips and Array Analyses -Expression Arrays , Comparative Analyses between Species and Strains Proteomics: 'Proteome' of an Organism . Medical applications: Genetic Disease -Pharmaceutical and Biotech Industry. Forensic applications. Agricultural applications POTENTIAL OF BIOINFORMATICS The potential of Bioinformatics in the identification of useful genes leading to the development of new gene products, drug discovery and drug development has led to a paradigm shift in biology and biotechnology-these fields are becoming more & more computationally intensive. The new paradigm, now emerging, is that all the genes will be known "in the sense of being resident in database available electronically", and the starting point of biological investigation will be theoretical and a scientist will begin with a theoretical conjecture and only then turning to experiment to follow or test the hypothesis. With a much deep understanding of the biological processes at the molecular level, the Bioinformatics scientist have developed new techniques to analyze genes on an industrial scale resulting in a new area of science known as 'Genomics'. THREE LEVELS OF BIOINFORMATICS 1- Analysis of a single gene (protein) sequence. For example: Similarity with other known genes. Phylogenetic trees; evolutionary relationships 2- Analysis of complete genomes. For example: Which gene families are present, which missing? Location of genes on the chromosomes, correlation with function or evolution 3- Analysis of genes and genomes with respect to functional data. For example: Expression analysis; microarray data; mRNA conc. measurements Identification of essential genes, or genes involved in specific processes BIOLOGICAL DATABASE A biological database is a large, organized body of persistent data, usually associated with computerized software designed to update, query, and retrieve components of the data stored within the system. A simple database might be a single file containing many records, each of which includes the same set of information. For example, a record associated with a nucleotide sequence database typically contains information such as contact name; the input sequence with a description of the type of molecule; the scientific name of the source organism from which it was isolated; and, often, literature citations associated with the sequence. For researchers to benefit from the data stored in a database, two additional requirements must be met: • Easy access to the information; and • A method for extracting only that information needed to answer a specific biological question. Currently, a lot of bioinformatics work is concerned with the technology of databases. These databases include both "public" repositories of gene data like GenBank or the Protein DataBank (the PDB), and private databases like those used by research groups involved in gene mapping projects or those held by biotech companies. A few popular databases are GenBank from NCBI (National Center for Biotechnology Information), SwissProt from the Swiss Institute of Bioinformatics and PIR from the Protein Information Resource. TOOLS OF BIOINFORMATICS There are both standard and customized products to meet the requirements of particular projects. There are data-mining software that retrieve data from genomic sequence databases and also visualization tools to analyze and retrieve information from proteomic databases. Homology and Similarity Tools: Homologous sequences are sequences that are related by divergence from a common ancestor. Thus the degree of similarity between two sequences can be measured while their homology is a case of being either true of false. This set of tools can be used to identify similarities between novel query sequences of unknown structure and function and database sequences whose structure and function have been elucidated. EG- BLAST APPLICATION PROGRAMMES IN BIOINFORMATICS JAVA in Bioinformatics: Since research centers are scattered all around the globe ranging from private to academic settings, and a range of hardware and OSs are being used, Java is emerging as a key player in bioinformatics. Physiome Sciences' computer-based biological simulation technologies and Bioinformatics Solutions' PatternHunter are two examples of the growing adoption of Java in bioinformatics. Perl in Bioinformatics: String manipulation, regular expression matching, file parsing, data format interconversion etc are the common text-processing tasks performed in bioinformatics. Perl excels in such tasks and is being used by many developers.Developers have designed several of their own individual modules for the purpose, which have become quite popular and are coordinated by the BioPerl project. BIOINFORMATICS PROJECT BioJava: The BioJava Project is dedicated to providing Java tools for processing biological data which includes objects for manipulating sequences, dynamic programming, file parsers, simple statistical routines, etc. BioPerl: The BioPerl project is an international association of developers of Perl tools for bioinformatics and provides an online resource for modules, scripts and web links for developers of Perl-based software. BioXML: A part of the BioPerl project, this is a resource to gather XML documentation, DTDs and XML aware tools for biology in one location. Biocorba: CORBA is one such framework for interlanguage support, and the biocorba project is currently implementing a CORBA interface for bioperl. BIOINFORMATICS IN INDIA Studies of IDC points out that India will be a potential star in bioscience field in the coming years after considering the factors like bio-diversity, human resources, infrastructure facilities and government’s initiatives. According to IDC, bioscience includes pharma, Bio-IT (bioinformatics), agriculture and R&D. IDC has been reported that the pharmaceutical firms and research institutes in India are looking forward for cost-effective and high-quality research, development, and manufacturing of drugs with more speed. Bioinformatics has emerged out of the inputs from several different areas such as biology, biochemistry, biophysics, molecular biology, biostatics, and computer science. This sector is the quickest growing field in the country. The vertical growth is because of the linkages between IT and biotechnology, spurred by the human genome project. The promising start-ups are already there in Bangalore, Hyderabad, Pune, Chennai, and Delhi. There are over 200 companies functioning in these places. IT majors such as Intel, IBM, Wipro are getting into this segment spurred by the promises in technological developments BIOINFORMATICS AND IT’S SCOPE Bioinformatics has evolved into a full-fledged scientific discipline over the last decade. The definition of Bioinformatics is not restricted to computational molecular biology and computational structural biology. It now encompasses fields such as comparative genomics, structural genomics, transcriptiomics, Proteomics, cellunomics and metabolic pathway engineering. Developments in these fields have direct implications to healthcare, medicine, discovery of next generation drugs, development of agricultural products, renewable energy, environmental protection etc. Bioinformatics integrates the advances in the areas of Computer Science, Information Science and Information Technology to solve complex problems in Life Sciences. The core data comprises of the genomes and proteomes of human and other organisms, 3-D structures and functions of proteins, microarray data, metabolic pathways, cell lines & hybridoma, biodiversity etc. CONCLUSION Bioinformatics has a key role to play in the cutting edge Research & Development areas such as functional genomics, proteomics, protein engineering, pharmacogenomics, discovery of new drugs and vaccines, molecular diagnostic kits, agro-biotechnology etc. It has now been universally recognized that Bioinformatics is the key to the new grand data-intensive molecular biology that will take us into 21 century. A Bioinformatician must acquire/possess expertise in the essential multi-disciplinary fields that comprise the core of this new science. Quality research and education in Bioinformatics are vital not only to meet the existing challenges but also to set and accomplish new goals in Life Sciences. THANK YOU THANK YOU ANY QUESTION ?
Pages to are hidden for
"bioinformatics"Please download to view full document