Bio-informatics Projects

Bio-informatics Projects

1. Bio-informatics resource and application facility (BRAF) is setup at Centre For Development of Advanced Computing (CDAC) at Pune. 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.

2. Bioinformatics & Applied Biotechnology (IBAB), Bangalore developed 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.

3. IIT, Delhi developed 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 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.

4. IBAB, Bangalore developed 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.

5. National Botanical Research Institute (NBRI), Lucknow developed web base software tools for digitization and identification of RET (Rare, Endemic and Threatened) species and varieties.

6. Biotechnology Centre J.N. Krishi Vishwa Vidyalaya, Jabalpu developed 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.

7. 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.

8. 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.

9. ATP synthase is a membrane enzyme playing a crucial role in biological energy metabolism. JNU New Delhi is implemented 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.

10. Zinc finger motifs take part in protein–protein and protein–nucleic acid interactions in various protein groups including those involved in DNA repair. Bioinformatics Centre, Pondicherry University developed a database of Zinc Finger (ZF) motif designs and their corresponding 3-4 bp DNA recognition sequences, developed a software tool for designing ZFs for unique and gene-specific ZF target sites for all known genes encoded by the human genome.

11. Centres of Excellence for Research and Training in Bioinformatics at IBAB Bangalore, Bioinformatics Centres at Pune and Pondicherry Universityt. Has completed 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 etc.

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

13. 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 has been completed at Institute of Bioinformatics & Applied Biotechnology (IBAB), Bangalore

14. National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram, a constituent Laboratory of CSIR, has impleted a programme with the aim of developing a futuristic software platform for Cancer simulation.

15. A comparative analysis of the microbial (bacterial and fungi) diversity of Cherrapunjee (degraded land) and Mawsynram sacred grove in Meghalaya was undertaken at Department of Biotechnology & Bioinformatics, North Eastern Hill University, Shillong. Microbial database matching the landscape and ecology. Sophisticated bio-informatics tools and wet lab procedures are used in this study of microbes.

16. With the aim of improving the annotation of agriculturally important plant genome a project has been implemented at Bharathidasan University, Tiruchirappalli.

17. 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. Research paper published in the current Science issue and efforts are on to develop web server for the same.

18. Developed a database of functionally diverse Type III Polyketide Synthase(PKS) protein structures with specific catalytic functions 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.

19. A concerted approach to raise awareness about bio-informatics application and augmenting skills for its implementation in agriculture research and crop productivity improvement has been implemented 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

20. A project has been completed 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.

21. A project has been setup to develop a web server for predicting hub proteins along with an associated secondary database of interacting proteins.

22. A project has been completed with the objective of predicting sub cellular localization using artificial intelligence.

23. Bhartiar University, Coimbatore developed 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 etc.

24. IIT, Guwahat developed a systematic Germplasm collection, inventorization of ginger germplasm and then generate barcode data and assembly using plant specific barcode. Significant developments have been made in Germplasm collection, DNA isolation and quantification and PCR analysis.

25. IIT, Guwahati, developed 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.

26. Tea Research association Jorhat, Assam developed physical mapping of Tea using BAC (Bacterial Artificial Chromosome) library and Management, Germplasm and mapping populations. Constructed a high density transcript map of Tea also features in the target list

27. Software on microbial diversity of NE India exploring different sites in the northeastern states a has been developed by North Eastern Hill University, Shillong

28. 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 has been implemented.

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