Project titles for:
Project titles for: 2008-10
- In silico analysis of Larger subunit of AGPase in Rice and Maize
- In silico Analysis of mutated in Larger subunit of AGPase in Maize
- Structural Comparison of Betaine Aldehyde Dehydrogenase-1 of Barley and Rice
- Analysis of Gene Expression Database of Skin Cancer
- Evaluation of Sequence Alignment Tools
- Phylogenetic analysis of Drb 3.2 gene
- Modelling of Smaller subunit of AGPase in Rice and Maize
- Prediction of Protein structure from sequence
- Development of Clinical Information Database of domestic animals
- To identify distant relationship between flavoprotein superfamily
- Promoters comparison in bacteria
- Transport protein features analysis
- Genome deciphering and comparative genomics of Solanaceous genome
- Computational approach in deciphering effect of gene alteration inArabidopsis Thaliana
- Simulation of conformational changes in protein
The objective of the present work was to compare a representive dataset of promoters of Salmonella typhimurium LT2. For this, 461 genes including essential genes and genes with various sigma factors were selected. The information about the operon and strand on which they are transcribed was retrieved from MicrobesOnline database. The nucleotide sequences (with -250 upstream and +250 downstream region) were downloaded from the same database which receives sequences from NCBI. Using Neural Network Promoter prediction (NNPP), promoters were predicted. These predicted promoters were compared to reveal the pattern and degree of conservation of nucleotides at various positions in the promoter region. First all the 461 genes were compared using a tool named Data Analysis in Molecular Biology and Evolution (DAMBE) to reveal the presence of specific nucleotides in the -10 region showing the highest degree of conservation. A consensus of TATAAT (-11 to -6) was observed showing highest frequency for nucleotide âTâ at -6 position. The -35 region was not clearly defined. Promoters of various sigma-dependent genes were then compared individually to detect any other important positional conservation of nucleotides. Although, the comparison of different sigma-dependent promoters had not resulted in very fruitful results for -35 region but it revealed various degree of conservation of different nucleotides in the -10 region. The generalizations observed from this study of promoters can be very helpful in the development of promoter finding programs and this study of Salmonella typhimurium can be taken further to understand and experiment on the transcription and gene expression.