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Bioinformatics Division
(Sponsored by DBT, Govt. of India)
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Under the BTIS net programme of DBT, a Bioinformatics Center titled "Distributed Information Sub-Centre (DISC)" has been established in October, 2002 in IICB.
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Team Members :
Dr. Chitra Dutta – Coordinator
Mr. Sanjib Chatterjee – Project Assistant
Mr. Sandip Paul – Project Assistant
Mr. Sumit K. Bag – Project Assistant |
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Objectives
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To build up information resource on biotechnology/genomics/proteomics and to develop relevant information handling tools and techniques.
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To develop and conduct original research programmes on in silico biology (especially in the areas of genome analysis and metagenomics).
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To provide a national bio-information network designed to bridge the interdisciplinary gaps in biotechnology information.
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To facilitate and enhance application of bioinformatics in life science research and to provide bioinformatics related technical support services to the national community of users.
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To organize long-term/short-term training programmes in diverse application of bioinformatics and computational biology.
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Computing facilities
Hardware
- SGI Octane Workstations
- High End Server (Itenium II Hp Integrity Server 4640), Linux OS
- Mail Server (Xeon server)
- Ftp Server (Xeon server)
- P4 PCs
- Laser Printers
- DeskJet Printers
- High speed Network Printer (200 Mb) with Copier and Scanner function
- High Resolution Scanners
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Software
In-House Software Development Activity
Novel algorithms and programs are being developed by the members of the centre for macromolecular sequence analysis. Among the in-house software tools currently available at the Centre are : |
(A) GCA & ClusterViz - A pair of programs, developed in C++ and Perl, for clustering of protein/gene sequences based on Markov-Chain Monte Carlo simulation and integrated visualization of the clusters with hyperlinks to their taxonomic distributions and functional annotations
(B) SPAST (Substitution Pattern Analysis Software Tool) - An integrated software tool for quantitative analysis of (i) Nucleotide Substitution (synonymous/ non-synonymous/ non-coding) Patterns (ii) Amino Acid Substitution Patterns and (iii) changes in propensities for secondary structure formation in orthologous or paralogous genes/gene-products
(C) PROCGR - A PC-based software tool, written in GWBASIC, developed for generation of Chaos Game Representation (CGR) patterns of different families of proteins.
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Commercially acquired software packages :
- Insight II Platform in Silicon Graphics Octane (Version 2000.1)
Modules:
Homology Modeling
Delphi
Biopolymer
DOCKING
- GCG Wisconsin Package (Version 10.3) & SeqWeb (Version 2.1) (Sequence Analysis Package)
- DNA Star Laser gene (Genome and Protein Sequence Analysis)
- DS Gene (Version 1.5) - (A suite of protein modeling & simulation tools)
- Statistica (Version 6) (Statistical Analysis Package)
- Corel Draw
- Visual Studio .NET
- End Note (Version 8.0.2 )
- Sigma plot (Version 9.0)
- Adobe Creative Suite
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Recent P&I
- Das S, Paul S, Chatterjee S, Dutta C. (2005) Codon and amino Acid usage in two major human pathogens of genus bartonella -- optimization between replicational-transcriptional selection, translational control and cost minimization. DNA Res., 12:91-102.
- Das S, Ghosh S, Pan A, Dutta C. (2005) Compositional variation in bacterial genes and proteins with potential expression level. FEBS Lett.;579 :5205-5210.
- Chanda I, Pan A, Dutta C. (2005) Proteome composition in Plasmodium falciparum: higher usage of GC-rich nonsynonymous codons in highly expressed genes.J Mol Evol. 61:513-23.
- Das S, Pan A, Paul S, Dutta C. Comparative analyses of codon and amino acid usage in symbiotic island and core genome in nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum. J Biomol Struct Dyn. 2005 ; 23(2):221-232.
- Das S, Paul S, Dutta C. (2006) Synonymous codon usage in Adenoviruses: Influence of mutation, selection and protein hydropathy. Virus Res. 117, 227-36.
- Das S, Paul S, Dutta C. (2006) Evolutionary constraints on codon and amino acid usage in two different strains of human pathogenic Actinobacteria Tropheryma whipplei. J Mol Evol. 62, 645-58.
- Das S, Paul S, Bag S. K., Dutta C. (2006) Analysis of Nanoarchaeum equitans genome and proteome composition: Indications for hyperthermophilic and parasitic adaptation. BMC Genomics. 7, 186.
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