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Introduction to Bioinformatics (Elective) – SBB1609 SCHOOL OF BIO AND CHEMICAL ENGINEERING DEPARTMENT OF BIOTECHNOLOGY Unit 1 – Introduction to Bioinformatics (Elective) – SBB1609 1 I HISTORY OF BIOINFORMATICS Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biologicaldata. As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics, and engineering to analyze and interpret biological data. Bioinformatics has been used for in silico analyses of biological queries using mathematical and statistical techniques. Bioinformatics derives knowledge from computer analysis of biological data. These can consist of the information stored in the genetic code, but also experimental results from various sources, patient statistics, and scientific literature. Research in bioinformatics includes method development for storage, retrieval, and analysis of the data. Bioinformatics is a rapidly developing branch of biology and is highly interdisciplinary, using techniques and concepts from informatics, statistics, mathematics, chemistry, biochemistry, physics, and linguistics. It has many practical applications in different areas of biology and medicine. Bioinformatics: Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data. Computational Biology: The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems. "Classical" bioinformatics: "The mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information.” The National Center for Biotechnology Information (NCBI 2001) defines bioinformatics as: "Bioinformatics is the field of science in which biology, computer science, and information technology merge into a single discipline. There are three important sub- disciplines within bioinformatics: the development of new algorithms and statistics with which to assess relationships among members of large data sets; the analysis and interpretation of various types of data including nucleotide and amino acid sequences, protein domains, and protein structures; and the development and implementation of tools that enable efficient access and management of different types of information 2 Even though the three terms: bioinformatics, computational biology and bioinformation infrastructure are often times used interchangeably, broadly, the three may be defined as follows: 1. bioinformatics refers to database-like activities, involving persistent sets of data that are maintained in a consistent state over essentially indefinite periods of time; 2. computational biology encompasses the use of algorithmic tools to facilitate biological analyses; while 3. bioinformation infrastructure comprises the entire collective of information management systems, analysis tools and communication networks supporting biology. Thus, the latter may be viewed as a computational scaffold of the former two. There are three important sub-disciplines within bioinformatics: • the development of new algorithms and statistics with which to assess relationships among members of large data sets; • the analysis and interpretation of various types of data including nucleotide and amino acid sequences, protein domains, and protein structures; • and the development and implementation of tools that enable efficient access and management of different types of information Bioinformatics definition - other sources • Bioinformatics or computational biology is the use of mathematical and informational techniques, including statistics, to solve biological problems, usually by creating or using computer programs, mathematical models or both. One of the main areas of bioinformatics is the data mining and analysis of the data gathered by the various genome projects. Other areas are sequence alignment, protein structure prediction, systems biology, protein-protein interactions and virtual evolution. (source: www.answers.com) • Bioinformatics is the science of developing computer databases and algorithms for the purpose of speeding up and enhancing biological research. (source: www.whatis.com) • "Biologists using computers, or the other way around. Bioinformatics is more of a tool 3 than a discipline.(source: An Understandable Definition of Bioinformatics , The O'Reilly Bioinformatics Technology Conference, 2003) (4) • The application of computer technology to the management of biological information. Specifically, it is the science of developing computer databases and algorithms to facilitate and expedite biological research.(source: Webopedia) • Bioinformatics: a combination of Computer Science, Information Technology and Genetics to determine and analyze genetic information. (Definition from BitsJournal.com) • Bioinformatics is the application of computer technology to the management and analysis of biological data. The result is that computers are being used to gather, store, analyse and merge biological data.(EBI - 2can resource) • Bioinformatics is concerned with the creation and development of advanced information and computational technologies to solve problems in biology. • Bioinformatics uses techniques from informatics, statistics, molecular biology and high-performance computing to obtain information about genomic or protein sequence data. Bioinformaticist versus a Bioinformatician A bioinformaticist is an expert who not only knows how to use bioinformatics tools, but also knows how to write interfaces for effective use of the tools. A bioinformatician , on the other hand, is a trained individual who only knows to use bioinformatics tools without a deeper understanding. Aims of Bioinformatics In general, the aims of bioinformatics are three-fold. 1. The first aim of bioinformatics is to store the biological data organized in form of a database. This allows the researchers an easy access to existing information and submit new entries. These data must be annoted to give a suitable meaning or to assign its functional characteristics. The databases must also be able to correlate between different hierarchies of information. For example: GenBank for nucleotide and protein sequence information, Protein Data Bank for 3D macromolecular structures, etc. 4 2. The second aim is to develop tools and resources that aid in the analysis of data. For example: BLAST to find out similar nucleotide/amino-acid sequences, ClustalW to align two or more nucleotide/amino-acid sequences, Primer3 to design primers probes for PCR techniques, etc. 3. The third and the most important aim of bioinformatics is to exploit these computational tools to analyze the biological data interpret the results in a biologically meaningful manner. Goals The goals of bioinformatics thus is to provide scientists with a means to explain 1. Normal biological processes 2. Malfunctions in these processes which lead to diseases 3. Approaches to improving drug discovery To study how normal cellular activities are altered in different disease states, the biological data must be combined to form a comprehensive picture of these activities. Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data. This includes nucleotide and amino acid sequences, protein domains, and protein structures. The actual process of analyzing and interpreting data is referred to as computational biology. Important sub-disciplines within bioinformatics and computational biology include: • Development and implementation of computer programs that enable efficient access to, use and management of, various types of information • Development of new algorithms (mathematical formulas) and statistical measures that assess relationships among members of large data sets. For example, there are methods to locate a gene within a sequence, to predict protein structure and/or function, and to cluster protein sequences into families of related sequences. The primary goal of bioinformatics is to increase the understanding of biological processes. What sets it apart from other approaches, however, is its focus on developing and applying 5 computationally intensive techniques to achieve this goal. Examples include: pattern recognition, data mining, machine learning algorithms, and visualization. Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein–protein interactions, genome-wide association studies, the modeling of evolution and cell division/mitosis. Bioinformatics now entails the creation and advancement of databases, algorithms, computational and statistical techniques, and theory to solve formal and practical problems arising from the management and analysis of biological data. Tools: Used in three areas • Molecular Sequence Analysis • Molecular Structural Analysis • Molecular Functional Analysis Over the past few decades, rapid developments in genomic and other molecular research technologies and developments in information technologies have combined to produce a tremendous amount of information related to molecular biology. Bioinformatics is the name given to these mathematical
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