CENTRE OF EXCELLENCE IN BIOINFORMATICS AT MKU

The main focus of the Centre of Excellence in Bioinformatics at Madurai Kamaraj University is on research and development, manpower training and services in the areas of proteomics, structural bioinformatics, software and database development. Manpower training is provided through the Advanced Diploma in Bioinformatics, Ph.D. training in related areas. Workshops, Seminars and courses on programming for Computational Biology, Structural Biology, and Bioinformatics offered as part of the Credit Based Choice System of the University to the post graduate students. The Virtual Private Network of the BTIS is used to make available the databases which we have developed as well as those that we are mirroring like SCOP (http://203.90.127.174:8081). The centre has collaborations with international institutions such as Weizmann Institute, Israel and University of Bath, UK. The centre has interaction with industries such as Amrutanjan, Avesthagen, Hindustan Lever etc., through consultancy and research projects by the faculty involved in the centre. So far, all the alloted manpower positions for the CoE have been recruited.

The collaborative research program of the CoE at MKU have resulted in publications in journals such as Nucleic Acids Research, FEBS Immunology and Medical Microbiology, Cellular and Molecular Life Sciences, In Silico biology, BMC Microbiology, Acta Crystallographica, and other journals. The research covers broadly the following areas of

  • Genomics, Proteomics and Structural Bioinformatics of selected regulatory systems in Streptomyces, Salmonella etc.,
  • Validation and annotation of databases of selected organisms and
  • Computational and experimental analysis of selected systems.
Some of the more recent work is brielfy described below.

Plasma Proteomics of leprosy has been initiated by Dr.K.Dharmalingam's group. Proteins which are differentially expressed were determined first by 2D electrophoresis and the selected protein spots were identified using MALDI TOF mass spectrometry. These proteins were identified by peptide mass finger printing. In doubtful cases MALDI MS/MS analysis was performed using seamless PSD analysis with Axima CFR plus MALDI TOF Mass spectrometer equipped with a CID tube. Bioinformatics of serum Proteomics of control populations including total annotation will be completed this year.

Detection of small RNAs in genomes, computational and characterization of the RNA binding protein HF-I (Hfq) are being carried out by Dr. Z.A. Rafi and his group. A comparative genomics study based on the 21 genomes of the Enterobacteriacae has been able to identify more than 100 new sRNAs.

Structural bioinformatics of prophage proteins and porins by Dr. S. Krishnaswamy and his group has resulted in a consensus approach to porin detection and the development of two methods to detect prophages in bacterial genomes. These have helped to develop two databases viz., the porin database (http://203.90.127.174:8081/PRNDS) and the prophage database (http://203.90.127.174:8082/prophagedb/). PRNDS (PoRiN Database Server) is a database of probable Porins (3182 sequences) derived from SwissProt and Trembl classified into 8/16/18 and 22 stranded probable porins. The prophage database entries contains a total of 226 prophage entries covering a total of 6,628 proteins. Extensive annotation has been carried out for the e14 prophage of E.coli. A simulation of the two component EnvZ-OmpR regulatory system in E.coli has been done using E-CELL as part of the systems biology approach to regulatory systems.