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LESSON 1: INTRODUCTION TO BIOINFORMATICS, HISTORY AND SCOPE OF BIOINFORMATICS Learning Outcomes After reading this students should able to:- UNIT 1 APPLICATIONS OF BIOINFORMATICS ã Understand and apply the basic principles that underpin ã computer science. Demonstrate a range of practical software development and other computing skills in accord with best modern engineering practice. acquaintance with current research interests. ã Pursue deeper study in specialist subjects and have an ã Demon
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  © Copy Right: Rai University 2A.501 1 INTRODUCTION TO BIOINFORMATICS AND IT UNIT 1APPLICATIONS OF BIOINFORMATICS LESSON 1:INTRODUCTION TO BIOINFORMATICS,HISTORY AND SCOPE OFBIOINFORMATICS Learning Outcomes After reading this students should able to:- ã Understand and apply the basic principles that underpincomputer science. ã Demonstrate a range of practical software development andother computing skills in accord with best modernengineering practice. ã Pursue deeper study in specialist subjects and have anacquaintance with current research interests. ã Demonstrate analytical and problem-solving skills, enablingthem to apply their knowledge in a wide variety of situations. ã Show self-motivation and the ability to work independentlyas well as being effective team members. ã Demonstrate a range of transferable skills includingcommunication, self-organization, and basic mathematicaland logical reasoning. ã Appreciate the wider context of computer science in society,in industry, and in academia.To begin my introduction to this chapter, I would like to ask you to erase everything that you have learned and heard aboutBioinformatics. Although you may think this is not a good wayof going about it, it will overall be helpful in attaining my goal.You may think this will make it harder for me to teach, or that Iam attempting to pollute your mind with my views, and withfalse information. However, I give you my word that I will domy best to do none of that. My purpose is to educate you. Iwant to give you everything you need to make an educateddecision, based on the facts, and from the point of view of everyone and everything. I will do this by giving you scientificinformation about each and every topic, views of scientists, anyrelevant comments from religious perspectives, and opinionsfrom the general population. This way, all your thoughts andquestions on any topic will be clearly answered.“Begin at the beginning and go on till you come to the end,then stop.” This, of course, is a good strategy to stick to, if youknow WHERE to begin. If you are a complete novice in anyfield. The best learning method according to me is the askingHow’s, Why’s and what’s and Where’s and who’s (The five W’s)on any topic.Well ……Let us begin with What is Bioinformatics? To understand the basic idea of bioinformatics, one mightthink of a written language. The text you are reading consists of a series of letters, words, sentences, and paragraphs. If you didnot know the meanings of the words and the rules of thelanguage, this page would just be a collection of meaninglesssymbols. Similarly, the first time scientists saw gene and proteinsequences, they saw a string of symbols with no clear meaningin terms of biological function. But now, bioinformatics isshowing us many things about what sequences mean. Usingbioinformatics, sequences are being used to reveal relationshipsamong different life forms that we could not find out any otherway. Bioinformatics is revealing the rules and meaning of alanguage that is new to human beings but in fact is billions of years old — the “Language of Life.”Bioinformatics is an important part of modern biology becauseit allows scientists useful, powerful ways to look at their data.It’s one thing to have several DNA sequences from differentorganisms written down on a piece of paper, but it’s quiteanother to have those sequences available in computer databasesand to be able to use computers to compare how similar thosesequences are, investigate what functions the DNA sequencesmight have, etc. Another important point is that the numberof available DNA sequences is growing exponentially, sobioinformatics work is becomingThere are several definitions for bioinformatics here I give myown definition. Bioinformatics is the Synergy of BiologyAnd Informatics which Means Bioinformatics > Bio+Informatics Biology : is the science that studies living organisms Informatics : In short Informatics is the application of computer science and information science to the managementand processing of data, information, and knowledge.In general in biology field we study the living organisms in invivo (In the body, in a living organism especially lab experi-ments.), in vitro (Outside a living organism Literally, “in glass,”i.e., in a test tube or in the laboratory) which involves muchtime consumption .We all are aware of by using InformationTechnology How time factor can be controlled in all theapplications for example your e-business. So the question hereis why cannot we computerize our biological techniques andhave the information technology advantage .The answer given isyes we can make it in silico (A process that is completed entirelyby the use of a computer.)You know that our biological data is massive information suchas nucleic acid (DNA/RNA) and protein sequences, structures,functions, pathways and interactions which has be stored,retrieved and analyzed properly. Bioinformatics has evolved intoa full-fledged multidisciplinary subject that integrates develop-ments in Information and Computer Technology as applied toBiotechnology and Biological Sciences. Bioinformatics usesComputer software tools for database creation, data manage-ment, data warehousing, data mining and globalcommunication networking. Bioinformatics is the recording,  2 2A.501 © Copy Right: Rai University INTRODUCTION TO BIOINFORMATICS AND IT annotation, storage, analysis, and searching/retrieval of nucleicacid sequence (genes and RNA’s), protein sequence and struc-tural information. This includes databases of the sequences andstructural information as well methods to access, search,visualize and retrieve the information.Function genomics, bimolecular structure, proteome analysis,cell metabolism, biodiversity, downstream, processing inchemical engineering, drug and vaccine design are some of theareas in which Bioinformatics is an integral component.Bioinformatics concern the creation and maintenance of databases of biological information whereby researchers canboth access existing information and submit new entries.The most pressing tasks in bioinformatics involve the analysisof sequence information. Computational Biology is the namegiven to this process, and it involves the following ã Finding the genes and Coding Sequences, Promoter regions,repeat regions etc in the DNA sequences of variousorganisms ã Developing methods to predict the structure and/orfunctionof newly discovered proteins and structural RNA sequences. ã Clustering protein sequences into families of relatedsequences and the development of protein models. ã Aligning similar proteins and generating Phylogenetic treesto examine evolutionary Sub-disciplines within Bioinformatics There are three important sub-disciplines within bioinformaticsinvolving computational biology: ã The development of new algorithms and statistics withwhich to assess relationships among members of large datasets; ã The analysis and interpretation of various types of dataincluding nucleotide and amino acid sequences, proteindomains, and protein structures and ã The development and implementation of tools that enableefficient access and management of different types of information Activities in bioinformatics we can split the activities inbioinformatics in two areas: ã The organization ã The analysis of biological data Organization ã The creation of databases of biological information ã The maintenance of these databases ã Today, we are sequencing tens of Millions of bases a year andundertaking to sequence whole organism genomes. Thegrowth of the sequence databases is an unbrokenexponential. ã The current size of the EMBL nucleotide database (release 42of March 1995 ) is a staggering 262,000,000 bases. ã The most important databases today in biology are probablythe protein sequence databases. Analysis The most pressing tasks in bioinformatics involve the analysisof sequence information. Computational Medicinal Chemistryis the name given to this process, and it involves the following: ã Development of methods to predict the structure and/orfunction of newly discovered proteins and structural RNAsequences. ã Clustering protein sequences into families of relatedsequences and the development of protein models. ã Aligning similar proteins and generating Phylogenetic treesto examineI hope you could get some concept about what isbioinformatics. Now I will try to define it even though it isdifficult .Why I am saying it is difficult to define isBioinformatics is a multi disciplinary concept. Is there only onedefinition of Bioinformatics? Absolutely not. Bioinformatics isa bright new field. This is exemplified in the lack of a standarddefinition for the word. I give you few definitions; all certainlyhave a high degree of validity. Definition of Bioinformatics Roughly, bioinformatics describes any use of computers tohandle biological information. In practice the definition used bymost people is narrower;Bioinformatics to them is a synonym for “computationalmolecular biology”- the use of computers to characterize themolecular components of living things. The Appropriate Definition “Classical” Bioinformatics “The mathematical, statistical and computing methods that aimto solve biological problems using DNA and amino acidsequences and related information. “The Loose” Definition There are other fields-for example medical imaging / imageanalysis which might be considered part of bioinformatics.There is also a whole other discipline of biologically inspiredcomputation; genetic algorithms, Artificial Intelligence, neuralnetworks. Often these areas interact in strange ways. Neuralnetworks, inspired by crude models of the functioning of nerve cells in the brain, are used in a program called PHD topredict, surprisingly accurately, the secondary structures of proteins from their primary sequences. What almost allbioinformatics has in common is the processing of largeamounts of biologically derived information, whether DNAsequences or breast X-rays.“We should not think all biological computing isbioinformatics, e.g. mathematical modeling is notbioinformatics, even when connected with biology-relatedproblems. In my opinion, bioinformatics has to do withmanagement and the subsequent use of biological information,particular genetic information.”Even though the three terms: bioinformatics , computational biology and bioinformation infrastructure are often times used interchange-ably, broadly, the three may be defined as follows:  © Copy Right: Rai University 2A.501 3 INTRODUCTION TO BIOINFORMATICS AND IT 1.Bioinformatics: refers to database-like activities, involvingpersistent sets of data that are maintained in a consistentstate over essentially indefinite periods of time; 2.Computational biology: encompasses the use of algorithmictools to facilitate biological analyses; while 3.Bioinformation infrastructure : comprises the entire collective of information management systems, analysis tools andcommunication networks supporting biology. Thus, thelatter may be viewed as a computational scaffold of theformer two We can define bioinformatics as the study of information contentand information flow in biological systems and processes. Ithas evolved to serve as the bridge between observations (data)in diverse biologically related disciplines and the derivations of understanding (information) about how the systems orprocesses function, and subsequently the application (knowl-edge). A more pragmatic definition in the case of diseases is theunderstanding of dysfunction (diagnostics) and the subsequentapplications of the knowledge for therapeutics and prognosis. Definitions Bioinformatics ã It is the application of computer technology to themanagement and analysis of biological data. The result isthat computers are being used to gather, store, analyze andmerge biological data. ã The application of computer technology to the managementof biological information. Specifically, it is the sciencefacilitates and expedites biological research, particularly in of developing computer databases and algorithms to genomics. ã The study of the application of computer and statisticaltechniques to the management of biological information. Ingenome projects, bioinformatics includes the developmentof methods to search databases quickly, to analyze DNAsequence information, and to predict protein sequence andstructure from DNA sequence data. ã The analysis of biological information using computers andstatistical techniques; the science of developing and utilizingcomputer databases and algorithms to accelerate and enhancebiological research. ã The science of informatics as applied to biological research.Informatics is the management and analysis of data usingadvanced computing techniques. ã (Computational biology). This word has not a cleardefinition. It involves the analysis and interpretation of dataand the development of algorithms and statistics. The termwas coined to encompass computer applications in biologicalsciences but is now used to mean rather different things,from artificial intelligence and robotics to genome analysis.The term was srcinally applied to the computationalmanipulation and analysis of biological sequence data (DNAand/or protein), but now tends also to be used to embracethe manipulation and analysis of 3d structural data. ã The use of computers to handle biological information. Theterm is often used to describe computational molecularbiology – the use of computers to store, search andcharacterize the genetic code of genes, the proteins linked toeach gene and their associated functions. ã The application of computational techniques to themanagement and analysis of biological information. ã The science that uses advanced computing techniques formanagement and analysis of biological data. Bioinformaticsis particularly important as an adjunct to genomic research,which generates a large amount of complex data, involvingbillions of individual DNA building blocks, and tens of thousands of genes. (SNP consortium). ã The science of managing and analyzing biological data usingadvanced computing techniques. Especially important inanalyzing genomic research data. ã The use of computers in solving information problems inthe life sciences. It mainly involves the creation of extensiveelectronic databases on genomes, protein sequences etc. Alsoinvolves techniques such as three-dimensional modeling of biomolecules and biological systems. ã Computational or algorithmic approaches to the analysis andintegration of genomic, proteomic, or chemical data residingin databases. Bioinformatics includes applications for theanalysis of DNA and protein sequence patterns andsimilarities, tools for t ã An interdisciplinary area at the intersection of biological,computer, and information sciences necessary to manage,process, and understand large amounts of data, for instancefrom the sequencing of the human genome, or from largedatabases containing information about plants and animalsfor use in discovering and developing new drugs. ã A scientific discipline that comprises all aspects of thegathering, storing, handling, analyzing, interpreting andspreading of biological information. Involves powerfulcomputers and innovative programs, which handle vastamounts of coding information on genes and proteins fromgenomics programmers. Comprises the development andapplication of computational algorithms for the purpose of analysis, interpretation, and prediction of data for the designof experiments in the biosciences. [cub] ã An emerging science that applies computer and databasetechnology to biological data. Used extensively in genomics,proteomics (the study of proteins and their interactions),and combinatorial chemistry to track ever-growing amountsof information. ã The discipline of obtaining information about genomic orprotein sequence data. This may involve similarity searchesof databases, comparing your unidentified sequence to thesequences in a database, or making predictions about thesequence based on current knowledge of similar sequences.Databases are frequently made publicly available through theinternet, or locally at your institution. ã The acquisition, storage, arrangement, analysis, display andcommunication of information related to the biology of living things, generally assisted by the use of computers. ã The science of informatics as applied to biological research.Informatics is the management and analysis of data using  4 2A.501 © Copy Right: Rai University INTRODUCTION TO BIOINFORMATICS AND IT advanced computing techniques. Bioinformatics isparticularly important as an adjunct to genomics research,because of the large amount of complex data this researchgenerates. ã The discipline of using computers to address informationproblems in the life sciences; it involves the creation of electronic data bases on genomes, protein sequences, etc. ã The science dealing with the classification, storage, retrieval,and analysis of genomic information. ã The field of study that relates to the collection, organizationand analysis of large amounts of biological data usingnetworks of computers and databases (usually with referenceto the genome project and DNA, rna or protein sequence orstructure information) ã The collection, organization and analysis of large amountsof biological data, using networks of computers anddatabases. ã Information about human and other animal genes andrelated biological structures and processes ã The management and analysis of data from biologicalresearch. ã The use of it to acquire, store, manage and analyze any typeof biological data. Today’s accelerated progress in geneticresearch is possible, in part, because of this combination of biology, powerful algorithm tools and immense databases. . ã  Is the application of computer technology to biology; a combinationof techniques and models in statistical, computational, and lifesciences to understand the significance of biological data. Bioinformatics is an interdisciplinary research area that is theinterface between the biological and computational sciences. Theultimate goal of bioinformatics is to uncover the wealth of biological information hidden in the mass of data and obtainsa clearer insight into the fundamental biology of organisms.This new knowledge could have profound impacts on fields asvaried as human health, agriculture, the environment, energyand biotechnology.Well students I hope you have got good idea after seeing thesemany definitions. See there are two areas in bioinformaticswherein you can stand that is either Bioinformaticist orBioinformatician. Now I give you the clear distinction inbetween these two areas and this is the option to you to choosewhere you want to shine.A bioinformaticis t is an expert who not only knows how touse bioinformatics tools, but also knows how to write inter-faces for effective use of the tools.A bioinformatician , on the other hand, is a trained individualwho only knows to use bioinformatics tools without a deeperunderstanding.Thus, a bioinformaticist is to *.omics as a mechanical engineer isto an automobile. A bioinformatician is to *.omics as atechnician is to an automobile.Now we well see why Bioinformatics is so important and whatare needs. Why is Bioinformatics Important? The Need for Bioinformatics: ã Whole Genome Analyses and Sequences ã Experimental Analyses involving Thousands of Genessimultaneously ã DNA Chips and Array Analyses ã Expression Arrays ã Comparative Analyses between Species and Strains ã Proteomics: ‘Proteome’ of an Organism ... 2D gels, MassSpec ã Medical applications: Genetic Disease ... SNPs ã Pharmaceutical and Biotech Industry ã Forensic applications ã Agricultural applicationsThe greatest challenge facing the molecular biology communitytoday is to make sense of the wealth of data that has beenproduced by the genome sequencing projects. Traditionally,molecular biology research was carried out entirely at theexperimental laboratory bench but the huge increase in the scaleof data being produced in this genomic era has seen a need toincorporate computers into this research process.Sequence generation, and its subsequent storage, interpretationand analysis are entirely computer dependent tasks. However,the molecular biology of an organism is a very complex issuewith research being carried out at different levels including thegenome, proteome, transcriptome and metabalome levels.Following on from the explosion in volume of genomic data,similar increase in data have been observed in the fields of proteomics,transcriptomics and metabalomics.The firstchallenge facing the bioinformatics community today is theintelligent and efficient storage of this mass of data. It is thentheir responsibility to provide easy and reliable access to thisdata. The data itself is meaningless before analysis and the sheervolume present makes it impossible for even a trained biologistto begin to interpret it manually. Therefore, incisive computertools must be developed to allow the extraction of meaningfulbiological informationThere are three central biological processes around whichbioinformatics tools must be developed: ã DNA sequence determines protein sequence ã Protein sequence determines protein structure ã Protein structure determines protein functionThe integration of information learned about this key biologicalprocess should allow us to achieve the long-term goal of thecomplete understanding of the biology of organisms.Now we will see few challenges of bioinformatics by which wecan know the importance of bioinformatics. Challenges of Bioinformatics ã Precise, predictive model of transcription initiation andtermination: ability to predict where and when transcriptionwill occur in a genome
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