K. SEKAR, Ph.D. BIOINFORMATICS CENTRE SUPERCOMPUTER EDUCATION AND RESEARCH INDIAN INSTITUTE OF SCIENCE BANGALORE 560 012 INDIA sekar@physics.iisc.ernet.in. slide 0

K. SEKAR, Ph.D. BIOINFORMATICS CENTRE SUPERCOMPUTER EDUCATION AND RESEARCH INDIAN INSTITUTE OF SCIENCE BANGALORE 560 012 INDIA sekar@physics.iisc.ernet.in.

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  • K. SEKAR, Ph.D. BIOINFORMATICS CENTRE SUPERCOMPUTER EDUCATION AND RESEARCH INDIAN INSTITUTE OF SCIENCE BANGALORE 560 012 INDIA sekar@physics.iisc.ernet.in Voice: (91)-80-2932469 FAX : (91)-80-3600683 (91)-80-3601409 (91)-80-3600551 IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar
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  • APPLICATIONS OF DATA MINING IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar
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  • Abstract Bioinformatics is one of the fastest growing interdisciplinary areas in the biological sciences and has explored in such a way that we need powerful tools to organize and analyze the data. An overview will be presented on the general features of data mining tools, techniques and its applications. IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar
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  • Bioinformatics is the fashionable new name for the field previously called computational biology.The name is preferred by many because it puts the emphasis on the data storage and analysis, rather than on the biology, and the field is really data driven. IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar
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  • The term Bioinformatics is used to encompass almost all computer applications in biological sciences, but was originally coined in the mid 1980’s for the analysis of biological sequence data. The quantity of known sequences data outweighs protein structural data and by virtue of the genome projects, sequence database are doubling in size every year. A key challenge of bioinformatics is to analyze the wealth of sequence data in order to understand the amassed information in term of protein structure function and evolution. Wherever possible, a range of different methods should be used, and the results should be married with all available biological information. IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar
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  • Comprises the entire collection of information management systems, analysis tools and communication networks supporting biology. Refers to database-like activities involving persistent sets of data that are maintained in a consistent state over essentially indefinite periods of time. Encompass the use of algorithmic tools to facilitate biological database analyses. IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar
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  • DATA MINING Datamining is defined as “exploration and analysis by automatic and semi-automatic means, of large quantities of data in order to discover meaningful patterns and rules”. IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar
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  • The central challenge is to derive maximum results from the wealth of data.This can be achieved by establishing and maintaining databases and providing search and analysis tools to interpret the data. IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar
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  • DATABASE Database is nothing but a collection of quantitative data resulting from experimental measurements or observations in various fields of science.Recently interest in database has been kindled through international efforts to organize and analyze the data and update the knowledge IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar
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  • A database is essentially just a store of information.They are usually in the form of simple files (just a flat file, say).You can shove information into this store or retrieve it from the store. IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar
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  • Derived Database One of the greatest challenges in database research is analyze the database in depth and create derived databases to meet the needs or demands without compromising the sustainability and quality of the existing database. Creating desired database is expected is expected to dramatically reduce the workload of the user community and will serve as a highly focused database. IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar
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  • IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar Packages developed at the Bioinformatics Centre Raman Building Indian Institute of Science Bangalore 560 012 Principal Investigator Dr. K. Sekar E-mail sekar@physics.iisc.ernet.in
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  • IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar Search Engines 144.16.71.10 / psstProtein Sequence Search Tool 144.16.71.2/bsddBiomolecules Segment Display Device 144.16.71.10/msgsMotif Search in Genome Sequence 144.16.71.2/ssepSecondary Structural Elements in Protein Programmers 1. S.Saravanan 2. A.Ajmal Khan 3. C.K.Rajesh 4. T.Kamaraj 5. P.Selvarani 6. V.Shanthi 7. S.Sirajuddin Sheik
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  • IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar Database with Search facility 144.16.71.2/lsdbLipase Structural Database 144.16.71.2/lysdbLysozyme Structural Database 144.16.71.2/asdb3D-Amylase Database 144.16.71.2/gsdbGlobin Structural Database Programmers 1. C.K.Rajesh 2. T.Kamaraj 3. P.Sundrarajan 4. P.Selvarani 5. V.Shanthi 6. A.S.Zahir Hussain 7. S.Sirajuddin Sheik
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  • IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar Software for Structure analysis & manipulation 144.16.71.146/cap Conformation Angles Package 144.16.71.146/rp Ramachandran Plot 144.16.71.146/wap Water Analysis Package 144.16.71.146/sem Symmetry Equivalent Molecules Generator 144.16.71.146/pdbgoodies PDBGOODIES 144.16.71.10/gpsm Geometrical Parameters for Small Molecules 144.16.71.146/mbd Measurability of Biovoet difference 144.16.71.146/dtf Distribution of Temperature Factor Programmers 1. C.K.Rajesh 2. T.Kamaraj 3. P.Sundarajan 4. P.Selvarani 5. V.Shanthi 6. S.Sirajuddin Sheik
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  • IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar Present Programmers S.S. Sheik S. Das V.G. Vijay J.J. Lakshmi Ch. K. Kumar C.C. Lingam K.S. Mohan S.A. Fernando S.K. Raja
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  • IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar Water Analysis Package (WAP) V.Shanthi, C.K.Rajesh,J.Jayalakshmi,V.G.Vijay & K.Sekar J.APPL.CRYST. (2003) 36, 167-168 Protein Sequence Search Tool (PSST 1.1) S.Saravanan,A.Ajmul Khan & K.Sekar CURR.SCIENCE, (2000) 550 – 552 PDB Goodies – A Web based GUI to manipulate Protein Data Bank files A.S.Z.Hussain,V.Shanthi,S.S.Sheik,J.Jeyakanthan,P.Selvarani &K.Sekar ACTA CRYST. (2002), D58, 1385 – 1386 Ramachandran Plot (RP) S.Sheik,P. Sundararajan,A.S.Z Hussain & K.Sekar BIOINFORMATICS (2002) 18, 1548-1549
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  • IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar CADB: Conformation Angles Data Base of proteins S.S. Sheik, P. Ananthalakshmi, G. Ramya Bhargavi & K. Sekar NUCL. ACIDS RES., (2003) 448-451 SSEP: Secondary Structural Elements of Proteins V. Shanthi, P. Selvarani, Ch. K. Kumar, C.S. Mohire & K. Sekar NUCL. ACIDS RES., (2003) (In the press) SEM: Symmetry Equivalent Molecules – A web based GUI to generate and visualize the macromolecules A.S.Z. Hussain, V. Shanthi, Ch. K. Kumar, C.K. Rajesh, S.S. Sheik & K. Sekar NUCL. ACIDS RES., (2003) (In the press) Biomolecules Segment Display Device (BSDD) P.Selvarani,V.Shanthi,C.K.Rajesh,S.Saravanan & K.Sekar J.MOL. GRAPHICS & MODELLING (2003) (in press)
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  • IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar Department of Biotechnology Ministry of Science & Technology Govt. of India, India & Jai Vigyan National Science Foundation Govt. of India, India
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  • IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar Professor M. Vijayan Professor N. Balakrishnan Professor S.M. Rao Professor S. Ramakumar Colleagues and Friends
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  • IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar President of Nagoya University Professor Takashi Yamane & Other members Biotechnology & Biomaterial Science
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