Bioinformatics De yeaa daa reer nal tuna Pea Pe he (internet) A my brain present my bod ae a joinformatics is the combination (or marriage!) of biology and information technology. Basically, bioinformatics is a recently developed science using information to understand biological phenomenon. It broadly involves the computational tools and methods used to manage, analyse and manipulate volumes and volumes of biological data. Bioinformatics may also be regarded as a part of the computational biology. The latter is concerned with the application of quantitative analytical techniques in modeling and solving problems in the biological _ systems. Bioinformatics is an interdisciplinary approach requiring advanced knowledge of computer science, mathematics and statistical methods for the understanding of biological phenomena at the molecular level. History and relevance of bioinformatics The term bioinformatics was first introduced in 1990s, Originally, it dealt. with the management and analysis cof the data pertaining to DNA, RNA and protein sequences. As the biological data’ is” being produced at an unprecedented rate, their management and interpretation invariably requires bioinformatics. Thus, bioinformatics now includes many other types of biological data, Some of the most important ones are listed below + Gene expression profiles © Protein structure + Protein interactions Microarrays (DNA chips) Functional analysis of biomolecules Drug designing. Bioinformatics is largely (not exclusively) a computer-based discipline, Computers are in fact very essential to handle large volumes. of biological data, their storage and retrieval, We have to accept the fact that there is no computer on earth (however advanced) which 609Medical Concepts/ Clinical Correlates © Bioinformatics has largely benefited biological and medical sciences, particularly related to ‘molecular biology and biotechnology. Some applications are listed : ‘@ Sequencing of macromolecules (proteins, DNA, RNA) ‘© Human genome sequencing fe Molecular modelling of biomolecules ‘¢ Handling of vast biological data ‘¢ Designing of drugs for the treatment of diseases # Development of models for the functioning of cells, tissues and organs ‘As such, there is no field of biological science that is not benefited by bioinformatics. can store information, and perform the functions like a living cell. Thus a highly complex information technology lies right within the cells of an organism. This primarily includes the organism’s genes and their dictates for the organisms biological processes and behaviour. BROAD COVERAGE OF BIOINFORMATICS Bioinformatics covers many specialized and advanced areas of biology. Functional genomics : Identification of genes and their respective functions. _- Structural genomics : Predictions related to functions of proteins. Comparative genomics : For understanding the genomes of different species of organisms. DNA microarrays : These are designed to measure the levels of gene expression in different tissues, various stages of development and in different diseases. Medical informatics : This involves the management of biomedical data with special reference to biomolecules, in vitro assays and clinical trials. COMPONENTS OF BIOINFORMATICS Bioinformatics comprises three Components 1. Creation of databases This the organizing, storage and management of the biological data sets. The . accessible to researchers to know the existing information and submit new entries. e.g, protein sequence data bank for molecular ftructure. Databases will be of no use until analysed. databases are 2. Development of algorithms and statistics : This involves the development of tools and resources to determine the relationship among the members of large data sets e.g. comparison of protein sequence data with the already existing protein sequences. 3. Analysis of data and interpretation : The appropriate use of components 1 and 2 (given above) to analyse the data and interpret the results in a biologically meaningful manner. This includes DNA, RNA and protein sequences, protein structure, gene expression profiles, and biochemical pathways. BIOINFORMATICS AND THE INTERNET The internet is an intemational computer network. A computer network involves a group of computers that can communicate (usually over a telephone system) and exchange data between users. It is the internet protocol (IP) that determines how the packets of information are addressed and routed over the network. To access the internet, a computer must have the correct hardware (modem/network card), appropriate software and permission for access to network. For this purpose, one has to subscribe to an internet service provider (ISP). World wide web (www) : www involves the exchange of information over the internet using a programme called browser. The most widely used browsers are Internet explorer and Netscape navigator.www works on the basis of Uniform resource locator (URL) which is a document with a unique address. URLs takes the format http,// (hypertext transfer protocol) that can identify the Nucleotid protocol for communication over www. biological databases are briefly described (Table 30.1). oa quence databases The nucleotide sequence data submitted by BIOLOGICAL DATABASES the or and genome sequencing groups is 7 an at the databases namely GenBank, EMBL oe of fhe biological data on a (European Molecular Biology Laboratory) and computer which can be manipulated to appear DDBJ (DNA Data Bank of Japan). There is a good in varying arrangements and subsets is regarded coordination between these three databases as as a database. The biological information can be they are synchronized on daily basis. stored in different databases. Each database has te coon webstie with ant : Besides the primary nucleotide databases site with unique navigation tools. (referred above), there are some other databases The biological databases are, in general, also to provide information on genes, genomes publicly accessible. Selected examples of and ongoing research projects. Table 30.1 Selected examples of ele ME elec im], Database(s) Salient features Primary nucleotide sequence databases GenBank Provides nucleotide sequence databases maintained by the (www.ncbi.nin.gov/GeneBank/) National Center for Biotechnology Information (NCBI), USA. Other nucleotide sequence databases UniGene The nucleotide sequences of GenBank in the form of clusters, (wivwncbi.nih.gov/UniGene/) representing genes are available. Genome Biology The information about the completed genomes is available. (www ncbi.nim.nih.gow/Genomes/) Protein sequence database SWISS-PROT Provides the description of the structure of a protein, its domains (www. expasy.ch/sport) structure, post-ranslational modifications, variants etc. It has high level of integration with other databases and minimal level of redundancy. Protein sequence motif databases PROSITE Provides information on protein families and domains. It also has (www.expasy.ch/prosite/) pattems and profiles for sequences and biological functions, Macromolecular databases PDB This is the primary database for 3-dimensional (3-D) structures: (www.resb.org/pdb) of biological macromolecules (determined by X-ray and NMR. studies). 2 Other databases es (KEC isa KEGG ‘The Kyoto Enoyclopedia of Genes and Genomes ( (wwrw.genome.ad.jp/kegg/) database with latest computerised information on biomolecules and cell biology. KEGG provides detalls on information pathways, interacting molecules and the connecting links with genes.Protein sequence databases Protein sequence databases are usually Prepared from the existing literature and/or in consultation with the experts. In fact, these databases represent the translated DNA. databases. Molecular structure of databases The three dimensional (3-D) structures of macromolecules are determined by X-ray crystallography and nuclear magnetic resonance (NMR). PDB and SCOP are the primary databases of 3-D structures of biological molecules. Other databases KEGG database is an important one that provides information on the current knowledge of molecular biology and cell biology with special reference to information on metabolic pathways, interacting molecules and genes. APPLICATIONS OF BIOINFORMATICS The advent of bioinformatics has revolutionized the advancements in biological science. And biotechnology is largely benefited by bioinformatics. The best example is the sequencing of human genome in a record time which would not have been possible without bioinformatics. A selected list of applications of bioinformatics is given below. + Sequence mapping of biomolecules (DNA, RNA, proteins). + Identification of nucleotide sequences of functional genes. + Finding of sites that can be cut by restriction enzymes. + Prediction of functional gene products. + To trace the evolutionary trees of genes. « For the prediction of 3-dimensional structure of proteins. + Molecular modelling of biomolecules. * Designing of drugs for medical treatment. + Handling of vast biological otherwise is not possible. data which + Development of models for the functioning various cells, tissues and organs. The above list of applications however, may be treated as incomplete, since at present there is no field in biological sciences that does not involve bioinformatics. SUMMARY ‘© Bioinformatics (a computer-based discipline) represents an alliance between biology and information technology. @ The storage, management and Interpretation of vast biological data invariably requires bioinformatics, @ Bioinformatics comprises three components-creation of data base, development of algorithms and statistics, and analysis of data and interpretation. © Biological databases, containing the biological information, are publicly accessible e.g. GenBank (www.ncbi.nth.gouGeneBank), © Bioinformatics has revolutionized the advancements of biological and medical sciences eg, sequencing of human genome. ee