Bio-informatics Projects

Department of Information Technology is supporting the following projects in the field of Bio-informatics:

Bio-informatics Resource and Application facility (BRAF) Phase II

Bio-informatics resource and application facility (BRAF) is setup at Centre For Development of Advanced Computing (CDAC) at Pune. The objective is to setup a Grid-enabled Bioinformatics Resource (Computing Power, Databases and the Software). At present Databases and software including teraflop computing power, terabyte storage with 10 Mbps bandwidth along with Bioinformatics Applications like Smith Waterman, BLAST, CLUSTAL W, Amber et al is provided.

Novel Algorithms for Sequence Alignment of Proteins and RNAs

A project is underway at of Bioinformatics & Applied Biotechnology (IBAB), Bangalore, with the objective to develop better sequenced alignment algorithms for protein and RNA to facilitate better structure predictions. The project has reported the development of algorithms for multiple sequence alignment and publication is underway.

Development of a Web-enabled Protein Structure Prediction Software

A project is underway at IIT, Delhi to develop a Web-enabled Protein Structure Prediction Software. A web enabled version for structure prediction titled Bhageerath software is now freely accessible to user communities. Visit www.scfbio-iitd.res.in.(External website that opens in a new window)

CG-Rex: Chaos Game Theory Based Open Source Tool  

A project on Open source tool based on Chaos Game Theory is currently developed at Bioinformatics Centre, Kerala University. The project is to develop a unique and specialized biosequence visualization tool named Chaos Game Representation explorer (C-GRex). The tool exclusively using Chaos Game Theory to visualize biological sequences and then analyze would offer a new way to handle the genomic and proteomic data. The tool is to be made available on the internet as an open source product. The software is already developed and hosted on BRAF Pune as open source software.

Developing a Software to Predict Expression Pattern of Genes Specific to Male Reproductive System

A project is implemented at IBAB, Bangalore to develop software to predict expression pattern of genes specific to male reproductive system from human and other mammalian genomes. This is to facilitate research on contraception and infertility treatments. The project has already developed a testis specific mammalian gene expression database which is hosted as open source on BRAF- CDAC Pune.

Indian Botanic Gardens Network

A project is currently underway at National Botanical Research Institute (NBRI), Lucknow for developing web base software tools for digitization and identification of RET (Rare, Endemic and Threatened) species and varieties. The multi-objective project aimed to develop a web enabled Indian Botanic Garden network, facilitating exchange of information among Indian Botanic Gardens, develop OS independent software for digitization of database on medicinal and RET plant species and tools for its automated identification. The project is well underway with data collection of 2000 species completed.

Development of a Software Tool to identify Ligand-Binding Site of 3D Structure of a Protein

A project is underway at Biotechnology Centre J.N. Krishi Vishwa Vidyalaya, Jabalpur to develop a unique cavity detection tool for identification of ligand-binding sites in proteins. The project aims to measure the efficacy of the tool to differentiate between probable cavities based on physicochemical properties, review the existing tools available to find out their capabilities and limitations. The identification and characterization of the ligand binding pockets of protein has been completed.

Bioinformatics Approach for Identification of Hypothetical ORF in Bacterial Genome & Hydrogen Production Pathways

The project aims to identify a hypothetical Open Reading Frame (ORF) in Hydrogen producing Bacterial Genome and Hydrogen production pathways crucial to improve the productivity and processing of microbial hydrogen production. The project initiated at AU-KBC Research Centre, Anna University Chennai has come out with databases of Eco-MP (Genome scale metabolic pathway database for Ecoli) and Rec- DB (re-annotated Ecoli database) that is hosted on BRAF Facility CDAC.

Targeted Anti-Cancer Lead Discovery: Virtual Screening (VS) Of Chemical Libraries Enriched In Natural Products

A project is implemented at Rajiv Gandhi Centre of Biotechnology Thiruvanthapuram for identification of small molecular inhibitors against 3 crucial molecular targets - WWP1, Stat3, and Stat5 which are the cause of a wide ranging tumours and leukaemia. This is done through computational screening (Virtual screening) of large databases of natural compounds along with their derivatives for quick recognition of lead molecules against the 3 molecular targets. Docking and scoring of screened compounds against WWPI is already completed and Docking of Stat3 and Stat 5 inhibitors are underway.

Development of Atomistic Approach for describing Excited States of Biological Systems: A Case Study on Proton Pumping Pathway of FO-F1 ATP Synthase

ATP synthase is a membrane enzyme playing a crucial role in biological energy metabolism. JNU New Delhi is implementing a project on Proton Pumping Pathway of FO-F1 ATP Synthase. The objectives behind this project are manifold. Understanding ATP Synthase mechanism, examining proton ATPase or proton pump, comprehending electrostatic gradient of proton movement, ascertain optical and transport mechanisms of functional proteins. At present molecular level calculations of the subunits of ATP structure is completed. Analysis of Zindo data on the mechanism of proton pump is underway.

Development of Software Tools for Designing Proteins to Engineer Plant and Mammalian Genomes

Zinc finger motifs take part in protein–protein and protein–nucleic acid interactions in various protein groups including those involved in DNA repair. A project is underway at Bioinformatics Centre, Pondicherry University to develop a database of Zinc Finger (ZF) motif designs and their corresponding 3-4 bp DNA recognition sequences, developing a software tool for designing ZFs for unique and gene-specific ZF target sites for all known genes encoded by the human genome. Software tool Bindpredict is already developed for identifying zinc finger nuclease binding sites. Efforts are on to project the binding sites graphically.

Centres of Excellence for Research and Training in Bioinformatics

DIT proposes to setup Centres of Excellence in Bioinformatics in Institutes of higher learning with world class infrastructure and faculty. Facilities should include state-of-the-art Wet labs. Centres have been set up at IBAB Bangalore, Bioinformatics Centres at Pune and Pondicherry University. The level of competence required from these institutes includes research projects to keep the country at the forefront of global Bioinformatics development. Research projects on understanding the molecular basis of Type 2 Diabetes mellitus, modeling folding mechanism of Amyloidogenic Proteins using computer simulation, prediction tool for identifying immune epitopes in an user-given protein sequence et al are currently underway.

Development of Computational Workflow for High Throughput Genome Analysis

A state-of-the art High Throughput Genome Analysis facility using a computational workflow environment is setup at Development of Advanced Computing (CDAC), Pune.  The trials of the facility are underway.

Development of Gene Expression Databases and Promoter Prediction Programs specific to Important Mammalian Tissues

With the objective of developing computer programs that can predict promoters and the expression pattern of genes that code for mRNA and/or proteins in specific mammalian tissues a program is underway at Institute of Bioinformatics & Applied Biotechnology (IBAB), Bangalore. The compilation of Mammalian gene expression database for some tissues has already been completed.

Developing an Agent Run-time Environment for Biological Simulations

National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram, a constituent Laboratory of CSIR, is implementing a programme with the aim of developing a futuristic software platform for Cancer simulation.  Agent based model for simulation of the basic immune system has been completed now Software design for the same is underway.

Comparative Analysis of Microbial Community in Meghalaya

A comparative analysis of the microbial (bacterial and fungi) diversity of Cherrapunjee (degraded land) and Mawsynram sacred grove in Meghalaya is undertaken at Department of Biotechnology & Bioinformatics, North Eastern Hill University, Shillong. This is to generate a microbial database matching the landscape and ecology. Sophisticated bio-informatics tools and wet lab procedures are used in this study of microbes.  Also in the pipeline is analyzing the biochemical potentials of a selected microbial group to understand their enzymatic activity and facilitate their production. Right now a dataset for microbial community is created. The project specifically aims at providing a baseline data on the microbial composition of Cherrapunjee which has suffered soli degradation.

Development of Twilight Zone Sequence Annotation Tool

With the aim of improving the annotation of agriculturally important plant genome a project is currently underway at Bharathidasan University, Tiruchirappalli. As a part of the project a prototype of twilight zone sequence annotation tool is to be build using Open Reading Frame (ORF), Threading methods like 3D-1D and five dimensional H3P2 method after suitable modifications.  Also part of the project is to develop a consensus method with Support Vector Machine (SVM) approach, to arrive at the appropriate homology. Currently PSSAlign and Predict fold tools have been developed and benchmarking is under progress.

Internet Computing Software to Detect Various Repeats in Genome and Protein Sequences

The project at IISc, Bangalore is implemented with the objective of creating high-end internet computing engines to analyze comprehensive biological data available as open literature. Developing powerful computing engines will be one of the major goals. The impetus is also on training for work on interdisciplinary projects.  At present an algorithm for sequentially separated motifs in Biological sequences has been developed, research paper published in the current Science issue and efforts are on to develop web server for the same.

Developing a Database of Type III Polyketide Synthase Protein Structures

Efforts are on to establish a database of functionally diverse Type III Polyketide Synthase(PKS) protein structures with specific catalytic functions. This project is underway at Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram. Computer simulation (In Silico analysis) of Type III polyketide synthase structural data is a major highlight of the project. At present Database structure with navigation facility has been completed. Also a tool to predict Type III PKS has been formulated and trials are underway for bettering its prediction accuracy.

Agri Bioinformatics Promotion Program

A concerted approach to raise awareness about bio-informatics application and augmenting skills for its implementation in agriculture research and crop productivity improvement is underway at various institutes across India. The Major focus is on molecular characterization of plants to come out with cures for disease pathogens, development of algorithm for gene annotation, a database on Indian IPR wheat genotypes et al. The participating institutes include S.D. Agriculture University, Gujarat, Central Plantation Crops Research Institute Kasargod, Kerala, Indira Gandhi Krishi Viswavidyala Raipur Chatisgarh, Assam Agriculture University, Jorhat and Directorate of Wheat Research, Karnal, Haryana

Designing Novel Anti-Malarial Drug Using Target Based Pharmacore Approach

A project is underway at JNU, New Delhi with the objective of designing pharmacophores and identifying scaffolds for known anti-malarial drugs and mapping protein-ligand interactions to improve success rate of potential drug molecules. The project got kick-started in June 2009.

Web server that Predicts Hub Proteins

Functionally important hub proteins are important for the robustness of the protein-protein network. A project has been setup to develop a web server for predicting hub proteins along with an associated secondary database of interacting proteins. The project got kick-started in July 2009. Kerala University has been assigned this project.

In Silico Prediction of Subcellular Localization

A project initiated in June 2009 is currently progressing at National Institute of Pharmaceutical Education and Research, Punjab with the objective of predicting sub cellular localization using artificial intelligence.

Text Mining and Data Warehousing of Protein Kinases Relationships and Pathways

Protein Kinases are supposed to be the key regulators of cell function which forms one of the largest as well as most functionally diverse gene families. The objective is to develop a computational text mining and data warehousing technology to gather as much information as possible of protein kinases, its relations with other genes and combine extracted information with DIP(Database of interacting proteins), KEGG, Genbank et al. The project implemented at Bhartiar University, Coimbatore was initiated in August 2009.

DNA Barcoding Based Biodiversity Inventory in Zingiberaceae of North East

Zingiberaceae or the ginger family is an important plant of northeast India. To develop a systematic Germplasm collection, inventorization of ginger germplasm and then generate barcode data and assembly using plant specific barcode markers is currently underway at IIT, Guwahati. Significant developments have been made in Germplasm collection, DNA isolation and quantification and PCR analysis.

Therapeutics against Leishmansiasis

A project is underway at IIT, Guwahati, with the objective of developing a structure prediction of target Enzymes of disease causing Leishmania parasite and then doing a structural analysis and comparison of modeled enzyme structures with mammalian enzymes. At present structural modeling of the target enzymes have been done and PDB files of Glutathione Synthatese of Leishmania submitted to Protein Model database. Optimization of docking procedure is in progress.

North East Project on Tea Bioinformatics

The objective is to do a physical mapping of Tea using BAC (Bacterial Artificial Chromosome) library and Management, Germplasm and mapping populations. Constructing a high density transcript map of Tea also features in the target list. The Project underway at Tea Research association Jorhat, Assam was initiated in August 2009.

Development of microbial database of NE India

With the objective of customization of software on microbial diversity of NE India exploring different sites in the northeastern states a project is underway at North Eastern Hill University, Shillong. The project is under progress.

North East Parasite Information and Analysis Centre- an In Silico Approach

In order to establish an integrated web based approach database related to parasitology and characterization of parasite biodiversity in mammalian livestock and animals used as food animals in northeast India a project is under progress at North Eastern Hill University, Shillong. At present collating of In Silico data from NCBI (National Center for Biotechnology Information) taxonomy and Entrez database is under progress. Designing of an integrated web server is also under progress.

For Further Information:

Ms. Alpana Dey

Director

Bioinformatics Initiative Division

TelePhone: +91-11-24301395, +91-11-24301231

e-Mail: adey AT mit.gov.in