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 CSIR-IICB.

 

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

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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