Bioinformatics

Introduction/Genesis of Programme

Department of Biotechnology started the Bioinformatics in 1987 as one of the thrust areas of Biotechnology and the sustained support has given impetus to the development of Bioinformatics in the country through establishing the necessary infrastructure including the ‘Supercomputer’. Over the time being, Bioinformatics has grown world over through contribution from various areas like Physics, Mathematics, Pharma sector and with the advent of new frontier area in Biotechnology like Genomics, Proteomics etc. As a result R&D activities in the relevant areas leads to massive inflow of data, which widens the scope of Bioinformatics, therefore, considering the international developments, the scope of the Bioinformatics is broadened and with wider scope, Department of Biotechnology has designated ‘Bioinformatics’ as ‘Theoretical and Computational Biology (TCB)’.

Bioinformatics in India is being used effectively for biology prospecting, conservation and management of bioresources, evaluation of products and processes and raw materials, managing complex data required to plan and monitor major national programmes and meeting the growing need of contract services and business outsourcing in Pharma and Biotechnology sectors. One of the major challenges in optimum exploration of Bioinformatics for solving life science issues is the formulation of appropriate computational biology problems that can be addressed through the IT tools. This requires adequate appreciation of the scope and strength of Bioinformatics by the biologist and basic understanding of the biological sciences by the computer and other information scientists. The solution lies in having adequate leaders with expertise both in life sciences and information technology as well as string institutional network tie-up between specialists from both the fields.

The need for Bioinformatics tools and expertise has increased as genome sequencing projects have resulted in an exponential growth of sequence databases. Data mining or Knowledge Discovery from Data (KDD) is a branch of Bioinformatics, Big data analysis for searching trends in data, helping to extract interesting, nontrivial, implicit, previously unknown and potentially useful information from data. The Biotechnology Information System Network (BTISnet) of this department has made several achievements towards Bioinformatics advancements in the country.

Aim/Objectives of the Programme

  • To provide a national bioinformation network designed to bridge the inter disciplinary gaps on Biotechnology information and establish link among scientists in organisations involved in R&D and manufacturing activities in the country.
  • To build up information resources, prepare databases on Biotechnology and to develop relevant information handling tools and techniques.
  • To continuously assess information requirements, organise creation of necessary infrastructure and to provide information and computer support services to the national community of users working in Biotechnology and allied areas.
  • To coordinate efforts to access Biotechnology information world wide including establishing linkages with some of the international resources of Biotechnology information (e.g. Databanks on genetic materials, published literature, patents, and other information of scientific and commercial value.
  • Perform research into advanced methods of computer based information processing for analyzing the structure and function of biologically important molecules.
  • To evolve and implement programmes on education of users and training of information scientists responsible for handling of Biotechnology information and its applications to Biotechnology research and development.
  • To establish regional cooperation amongst SAARC, and ASEAN countries for exchange of scientific information in Biotechnology through the development of appropriate network arrangements.

Biotechnology Information System Network (BTISNet):

The entire network has emerged as a very sophisticated scientific infrastructure for Bioinformatics involving state-of-the-art computational and communication facilities. The computer communication network, linking all the bioinformatics centres, is playing a vital role in the success of the bioinformatics programme. Database development, R&D activities in Bioinformatics, human resource development and a variety of services in support of Biotechnology R&D programmes and projects, has made this programme very popular and useful to the scientific community. At present, under this programme 152 Bioinformatics Centres are established in various Universities and Research Institutions spread across the country. The network centres are at various levels viz Centres of Excellence (CoEs), Distributed Information Centres (DICs), Distributed Information Sub-Centres (Sub-DICs) and Bioinformatics Infrastructure Facilities (BIFs).

The various areas in which the DBT’s Bioinformatics activity is winged out are as follows:
Details of Centre of Excellence

R&D in Bioinformatics

The Department has received many conceptualized project proposals for carrying out research in the field of Bioinformatics and Computational Biology. It has been witnessed that the generation of primary data have increased in the country with the support of several Government Departments like DBT. During this year, the Department has supported R&D projects which are specific to applications in the area of Agriculture, Medical and Knowledge Discovery from Data (KDD) by using Bioinformatics tools. The R&D projects which were supported earlier have also shown very good progress. The projects which had shown major outcomes in terms of scientific utility and product development are highlighted below.

Mango Database

Through a project supported to the Central Institute of Sub-Tropical Horticulture, Lucknow on Development of Genetic resource database and information system for mango, a database front-end has been developed using MySQL and PHP dealing with updating and retrieval of data. Data on morphological and molecular characterization was collected from NAGS and database on the mango accessions in different genebanks has been developed. The characterization data of 200 accessions was converted into codes and used for updating the data. Information on various aspects of Mangifera was collected and has been converted into digital format for adding it to the database. A website on Mango Genetic Resource Information System has been developed and is being tested for security options, so that it is enriched by uploading collected information as database with protection against unauthorized access.

Interactive Visual Diagnostic software to Check Nutrient Deficiency in Crops

An interactive Visual Diagnostic Software for the Identification of Nutrient Deficiencies in Crops is being implemented at TNAU, Coimbatore. A software has been developed based on the concept that plants are the indicator of nutrient deficiencies in soils that commensurate with a proverb “Face is the Index of the Mind”. The nutrient deficiencies exhibited by plants are very unique and distinguishable from one another depending on the mobility of ions and the physiological functions associated with it. To accomplish the task four approaches namely

  1. identification of nutrient deficiencies using visual symptoms in the field,
  2. classification based on dichotomous keys,
  3. confirmation through soil and plant analyses and
  4. scanning and integration of the images into the visual basic software.

Nutrient deficiency symptoms occurring in a wide array of crops (about 65) in seven agro-climatic zones of Tamil Nadu had been photographed using a high resolution digital camera. In the same location, soil and plant samples have been collected and analysed for its nutrient concentrations in order to relate whether symptoms associated with a particular nutrient deficiency. In maize, sugarcane, sorghum, soybean and groundnut, visual deficiency symptoms were graded and analyzed for their specific Fe and P concentrations. These experiments have reconfirmed that visual diagnosis closely coincides with the deficiency in soils vis-a-vis in plants. After confirmation, the photographic images were compressed by optimization process to reduce the file size to fit into the Visual Basic Software. The Visual Diagnostic Software has been developed and about 70% symptoms taken from the field had been integrated. Besides the software, a book on 'Diagnosis of Nutrient Deficiencies in Crops' in English and Tamil has been prepared to be able to provide basic information for the user groups.

Myocilin Structure Prediction using Knowledge based consensus.

A project on understanding protein aggregation in relation to Primary Open Angle Glaucoma (POAG) for evaluating models, screening polymorphisms and database development is being pursued jointly by MKU, Madurai and Aravind Eye Hospital Madurai. Mutations in Human Myocilin, a 55-kDa protein has been associated with open angle glaucoma. Most of these mutations are segregated to the olfactomedin-like domain. Only 2-4% of POAG patients have mutations in the myocilin gene. Understanding the structure and folding of the native protein and the mutants that increase aggregation could lead to possible prevention of the condition.

A plausible structure predicted for myocilin using a knowledge based consensus method was used to understand the role of myocilin and these mutations in POAG. The model resulted in a beta strand rich C-term Region (181 – 504) having the Cys245-Cys433 disulfide bone. Molecular dynamics is used to understand the role of the mutations in causing aggregation. For example, Gly367Arg a novel mutation has been identified in the patients from local population. From experimental analysis it has been shown that it aggregates in the trabecular meshwork and is not secreted out, whereas the normal protein is secreted out. Structural analysis and molecular dynamics calculations indicate how the mutation might cause possible conformational change leading to aggregation. A total of 124 genomic variations were screened and six polymorphisms that lead to altered protein products were detected as possible candidates for alternative splicing mechanism.

Flagship Consortium Projects on TB & Rice Bioinformatics

Two important flagship multi-agency and multi-institutional programs namely Development of Databases on TB & Rice have been conceptualized. Many well known institutions, say about 20 and scientists working in these areas are being associated with these projects for data sources and continuous evaluation at various stages of its implementations.

DBT e-Library Consortium (DeLCON)

The DBT’s Electronic Library Consortium (DeLCON) is a significant initiative of the Department of Biotechnology (DBT), Govt. of India, to enhance information resources in its research Institution. It was launched in January, 2009 with the ten DBT member-Institutions with large number prominent handpicked online journals. It is a topical endeavor for providing access to scholarly electronic resources including full-text and bibliographic databases in all the life science subject disciplines to the DBT Institutional community across the country. It facilitates access to high quality e-resources to research Institutions to enhance research, teaching and learning.

DeLCON provides current as well as archival access to more than 1000+ core peer-reviewed Biology and Biotechnology journals and a bibliographic database (SCOPUS) in different disciplines from 22 overseas publishers and aggregators. Presently there are 28 members and 20 publishers in this consortium.

The Faculties, Scientists, Research Scholars, Students and Project Assistants of Institutions covered under DeLCON are the primary beneficiaries. DBT sponsors the entire expenses for DBT organizations for providing e-Journals access through 'DeLCON Consortium'. This consortium has given value addition to the member scientific institutions in terms of access to more number of journals and saving of time as compared to the print version. The consortium has an excellent usage pattern. For more details log on to http://www.delcon.gov.in

Concerned Officer for more information

Programme HeadDr. Suchita Ninawe,Scientist G
Emailsninawe[at]dbt[dot]nic[dot]in
Phone No.011-24363722
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