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Bioinformatics Division
(Sponsored by DBT, Govt. of India)

Under the BTIS net programme of DBT, a Bioinformatics Center titled "Distributed Information Sub-Centre (DISC)" has been established in October, 2002 in IICB.
 

Team Members : 

Dr. Chitra Dutta             –    Coordinator
Mr. Sanjib Chatterjee  –    Project Assistant
Mr. Sandip Paul          –     Project Assistant
Mr. Sumit K. Bag         –    Project Assistant

 

Objectives

  • To build up information resource on biotechnology/genomics/proteomics and to develop relevant information handling tools and techniques.
  • To develop and conduct original research programmes on in silico biology (especially in the areas of genome analysis and metagenomics).
  • To provide a national bio-information network designed to bridge the interdisciplinary gaps in biotechnology information.
  • 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.
  • To organize long-term/short-term training programmes in diverse application of bioinformatics and computational biology.


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

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.

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
Recent P&I

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. Das S, Paul S, Dutta C. (2006) Synonymous codon usage in Adenoviruses: Influence of mutation, selection and protein hydropathy. Virus Res. 117, 227-36.
  6. 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.
  7. 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.
Animal House Publication & Information