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K. SEKAR, Ph.D. BIOINFORMATICS CENTRE SUPERCOMPUTER EDUCATION AND RESEARCH INDIAN INSTITUTE OF SCIENCE BANGALORE 560 012 INDIA

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Presentation on theme: "K. SEKAR, Ph.D. BIOINFORMATICS CENTRE SUPERCOMPUTER EDUCATION AND RESEARCH INDIAN INSTITUTE OF SCIENCE BANGALORE 560 012 INDIA"— Presentation transcript:

1 K. SEKAR, Ph.D. BIOINFORMATICS CENTRE SUPERCOMPUTER EDUCATION AND RESEARCH INDIAN INSTITUTE OF SCIENCE BANGALORE INDIA Voice: (91) FAX : (91) (91) (91) IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar

2 APPLICATIONS OF DATA MINING IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar

3 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

4 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

5 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

6 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

7 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

8 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

9 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

10 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

11 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

12 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 Principal Investigator Dr. K. Sekar

13 IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar Search Engines / psstProtein Sequence Search Tool /bsddBiomolecules Segment Display Device /msgsMotif Search in Genome Sequence /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

14 IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar Database with Search facility /lsdbLipase Structural Database /lysdbLysozyme Structural Database /asdb3D-Amylase Database /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

15 IISc Bioinformatics Centre & Supercomputer Education and Research Centre Applications of Data Mining – Dr. K. Sekar Software for Structure analysis & manipulation /cap Conformation Angles Package /rp Ramachandran Plot /wap Water Analysis Package /sem Symmetry Equivalent Molecules Generator /pdbgoodies PDBGOODIES /gpsm Geometrical Parameters for Small Molecules /mbd Measurability of Biovoet difference /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

16 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

17 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, 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,

18 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) 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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93 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

94 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

95 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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