Bioinformatics Facility/Tools

1. Proteomod: ProteoMod is a tool to quantitate protein post-translational phosphorylation modifications. The algorithm is based on the observation that the extent of shift in the migration distance of a protein on a 2D-PAGE due to certain number of phosphorylations is dependent, on both, the pI and the molecular weight of the native state of that protein. The extent of shift exhibited is then converted into the number of phosphorylations conferred and displayed as a result.

2. Plasmo2D: An ancillary proteomic tool to aid identification of proteins from Plasmodium falciparum. Bioinformatics tools to aid gene and protein sequence analysis have become an integral part of biology in the post-genomic era. Release of the Plasmodium falciparum genome sequence has allowed biologists to define the gene and the predicted protein content as well as their sequences in the parasite. Using pI and molecular weight as characteristics unique to each protein, we have developed a bioinformatics tool to aid identification of proteins from Plasmodium falciparum. The tool makes use of a Virtual 2-DE generated by plotting all the proteins from Plasmodium database on a pI versus molecular weight scale. Proteins are identified by comparing the position of migration of desired protein spots from an experimental 2-DE and that on a virtual 2-DE. The procedure has been automated in the form of user-friendly software called Plasmo2D.

3. Plasmo2Dbase: This is a relational Database containing important 2D-Gel images from our lab. It contain Gel images from Malarial Parasite Plasmodium falciparum.

4. Chaperone Networks: Recent years have seen the accumulation of a huge amount of information regarding the temporal and spatial expression of genes and proteins in the malarial parasite, Plasmodium falciparum. However, cellular functions result from the interactions of proteins with one another and with the environment at large, making it imperative to construct protein-protein interaction networks. Such networks have been constructed for P. falciparum using experimental as well as computational approaches. The advantage of constructing these networks lies in the ability to understand cellular processes at the systems level.

5. Next Generation Sequencing analysis: We have been expertizing in the “omics” generation utilizing the technology of Next Generation Sequencing and High-throughput Mass spectrometric analysis to enhance the current knowledge of science. We have successfully completed the whole genome sequencing of Candida auris and annotated its genome to define and compare its virulence factors to other known pathogenic fungus.

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