Project titles for:
Project titles for: 2010-12
- Multiple Sequence Alignment:Comparison and Evaluation
- Prediction of Codon Bias in Rice (Oryza sativa) genes
- Subunit-Subunit interactions in Heterotetrameric structure of rice (Oryza sativa) ADP Glucose pyrophosphorylase
- Identification of microRNA in rice (Oryza sativa)
- Virtual High-Throughput Screening of Peroxisome proliferator-activated receptor Inhibitors
- In silico idetentification and analysis of Simple Sequence Repeats (SSRs) in rice (Oryza sativa) ESTs
- Effect on virulence in Streptococcus pneumonia due to the presence of rlrA gene
Patterns and degrees of codon usage bias vary not only among different organisms, but also among genes in the same organism. Codon usage bias (CUB) convey useful information about the selection on synonymous codons induced by gene expression, translation efficiency and about the distinctive evolutionary properties. In the present study, by using 28502 complete coding sequences (CDS) of rice (Oryza sativa L.) with full length cDNA support, a detailed analysis of the codon bias was performed by employing Automated Codon Usage Analysis (ACUA) tool. 27897 genes demonstrated codon bias as their Enc ( effective number of codon) values varied from 20 to less than 61. On basis of GC3 content values, 267 biased genes were taken as high-GC3 (GC3>=0.8) whereas 27630 biased genes were termed as low-GC3 (GC3<0.8) genes. Quantification of genomic compositional asymmetry and dinucleotide frequency distribution analysis were further performed on selected biased genes to provide possible reasons of differences in nucleotide composition and compositional gradients along the coding regions of all the genes. GC3 gradient analysis results revealed that from the 5' end to 3' end of the open reading frame, high GC3 biased genes had a very slight positive gradient and low GC3 biased genes had strong negative gradient. CG3 skewness analysis showed that C3 preference even though higher for high GC3 genes than low GC3 genes, varied differentially as a function of distance from ATG codon. The analysis for CG3- and GC3- skewness as a function of distance from the start codon in rice genes clearly depicted the prevailing tendency for GC3 to decrease toward the 3' end. By dinucleotide frequencies ratio distribution analysis, 45/267 high GC3 biased genes were detected at CG/GC dinucleotide frequencies ratio peak centered at 1.1, whereas 1729/27630 and 1762/27630 low GC3 genes with CG/GC dinucleotide frequencies ratio peaks centered at 0.5 and 1.1, respectively were observed that clearly depicted that high GC3 genes had a significantly higher frequency of CG dinucleotides than low GC3 genes. The differential pattern of GC3 bias in rice genes shown in our study corroborate with the previous studies that plant codon usage might be affected by translational selection.