K. SEKAR, Ph.D. BIOINFORMATICS CENTRE SUPERCOMPUTER EDUCATION AND RESEARCH INDIAN INSTITUTE OF...

K. SEKAR, Ph.D.BIOINFORMATICS CENTRE

SUPERCOMPUTER EDUCATION AND RESEARCH INDIAN INSTITUTE OF SCIENCE

BANGALORE 560 012INDIA

[email protected]

Voice: (91)-80-2932469 FAX : (91)-80-3600683 (91)-80-3601409 (91)-80-3600551

Bioinformatics Centre & Supercomputer Education and Research Centre

Applications of Data Mining – Dr. K. Sekar

APPLICATIONS OF

DATA MINING

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.

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.

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.

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.

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”.

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.

DATABASEDatabase 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

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.

Derived DatabaseOne 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.

Packages developed at theBioinformatics Centre

Raman BuildingIndian Institute of Science

Bangalore 560 012

Principal InvestigatorDr. K. Sekar

E-mail [email protected]

Search Engines

144.16.71.10 / psst Protein Sequence Search Tool 144.16.71.2/bsdd Biomolecules Segment Display Device 144.16.71.10/msgs Motif Search in Genome Sequence 144.16.71.2/ssep Secondary Structural Elements in Protein

Programmers

1. S.Saravanan2. A.Ajmal Khan3. C.K.Rajesh4. T.Kamaraj5. P.Selvarani6. V.Shanthi7. S.Sirajuddin Sheik

Database with Search facility

144.16.71.2/lsdb Lipase Structural Database144.16.71.2/lysdb Lysozyme Structural Database144.16.71.2/asdb 3D-Amylase Database144.16.71.2/gsdb Globin Structural Database

Programmers

1. C.K.Rajesh2. T.Kamaraj3. P.Sundrarajan4. P.Selvarani5. V.Shanthi6. A.S.Zahir Hussain7. S.Sirajuddin Sheik

Software for Structure analysis & manipulation

144.16.71.146/cap Conformation Angles Package144.16.71.146/rp Ramachandran Plot144.16.71.146/wap Water Analysis Package144.16.71.146/sem Symmetry Equivalent Molecules Generator144.16.71.146/pdbgoodies PDBGOODIES144.16.71.10/gpsm Geometrical Parameters for Small

Molecules144.16.71.146/mbd Measurability of Biovoet difference144.16.71.146/dtf Distribution of Temperature Factor

Programmers

1. C.K.Rajesh2. T.Kamaraj3. P.Sundarajan 4. P.Selvarani5. V.Shanthi6. S.Sirajuddin Sheik

Present ProgrammersS.S. Sheik

S. DasV.G. Vijay

J.J. LakshmiCh. K. KumarC.C. LingamK.S. Mohan

S.A. FernandoS.K. Raja

Water Analysis Package (WAP)V.Shanthi, C.K.Rajesh,J.Jayalakshmi,V.G.Vijay & K.SekarJ.APPL.CRYST. (2003) 36, 167-168

Protein Sequence Search Tool (PSST 1.1)S.Saravanan,A.Ajmul Khan & K.SekarCURR.SCIENCE, (2000) 550 – 552

PDB Goodies – A Web based GUI to manipulate Protein Data Bank filesA.S.Z.Hussain,V.Shanthi,S.S.Sheik,J.Jeyakanthan,P.Selvarani &K.SekarACTA CRYST. (2002), D58, 1385 – 1386

Ramachandran Plot (RP)S.Sheik,P. Sundararajan,A.S.Z Hussain & K.SekarBIOINFORMATICS (2002) 18, 1548-1549

CADB: Conformation Angles Data Base of proteins S.S. Sheik, P. Ananthalakshmi, G. Ramya Bhargavi & K. SekarNUCL. ACIDS RES., (2003) 448-451

SSEP: Secondary Structural Elements of ProteinsV. Shanthi, P. Selvarani, Ch. K. Kumar, C.S. Mohire & K. SekarNUCL. ACIDS RES., (2003) (In the press)

SEM: Symmetry Equivalent Molecules – A web based GUI to generate and visualize the macromoleculesA.S.Z. Hussain, V. Shanthi, Ch. K. Kumar, C.K. Rajesh, S.S. Sheik & K. SekarNUCL. ACIDS RES., (2003) (In the press)

Biomolecules Segment Display Device (BSDD)P.Selvarani,V.Shanthi,C.K.Rajesh,S.Saravanan & K.SekarJ.MOL. GRAPHICS & MODELLING (2003) (in press)

Department of BiotechnologyMinistry of Science & Technology

Govt. of India, India

Jai Vigyan National Science Foundation

Govt. of India, India

Professor M. Vijayan

Professor N. Balakrishnan

Professor S.M. Rao

Professor S. Ramakumar

Colleagues and Friends

President of Nagoya University

Professor Takashi Yamane

Other members

Biotechnology & Biomaterial Science

K. SEKAR, Ph.D. BIOINFORMATICS CENTRE SUPERCOMPUTER EDUCATION AND RESEARCH INDIAN INSTITUTE OF...

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