Research activities which draw heavily on the Bioinformatics resources
Study of the proteome in the
blast fungus was initiated using high resolution 2D gels and the imaging
software for identification of protein differences. In addition to optimizing
the methods for proteome analysis in this fungus, several proteins crucial to
the establishment of the fungus on susceptible host have also been identified.
The glucose oxidase (GOX)
generated H2O2 induced/repressed proteins were identified
in the Oryza sativa L. database by sequence similarity searches in BLASTP
program. Protein domain analysis was performed using SMART (Shultz, J et al.,
1998) program to identify the conserved domains in these proteins. Also,
influence of GOX generated H2O2 on various agronomic
traits in the transgenic rice was calculated by using ANOVA of Prism 3.0 version
Using RasMOL Molecular graphics
program, visualization of proteins were done. We have created a resistance gene
(R) family database and identified the conserved domains in the resistance genes
by performing multiple sequence alignment using CLUSTALW program. Modelling of
Avr CO39 protein is under way to identify the interacting protein domains in the
gene products of resistance genes and avirulence gene.
Linkage analysis of blast
resistance genes and molecular markers (AFLP and SSLP) were done using Mapmaker
program version 3.0 (Lander et.al., 1987).
Pot2 fingerprints of Magnaporthe
grisea and % DLA obtained on RILs were analysed to perform cluster analysis
using UPGMA and SAHN programs of NTSYS-pc package. Correlation analysis by the
MXCOMP program was done for pair of similarity matrices to compare the
relationships within and among the M. grisea populations. Principal coordinate
analysis was performed on the basis of dice similarities with the procedure
DCENTRE of NTSYS-pc. Based on the analyses of the combined infection category (%
DLA) and Pot2 fingerprint profiles, different genetic lineages of M. grisea were
obtained. POPGENE and STATISTICA packages were used to calculated genetic
diversity, genetic distance, different, and gene flow etc., using Pot2
fingerprints M. grisea isolates.
STATGRAPHICS package was used to
optimize the growth conditions of yeast and bacteria for efficient production of
In order to study the microbial
diversity in the Jute retting environment, PCR amplification and sequencing of
16S rDNA from the DNA isolated from water used in retting was done. Sequence
similarity analysis was done by BLAST search in RDB (Ribosome Database Bank) to
identify the organisms present in jute retting environment.
Similarly, 16S rDNA analysis was
done to identify the soil microflora in the pesticide treated soils.