Genomics Inform.  2017 Mar;15(1):38-47. 10.5808/GI.2017.15.1.38.

Comparative Analysis of Predicted Gene Expression among Crenarchaeal Genomes

• Das S
• Chottopadhyay B
• Sahoo S

• KMID: 2375583
• DOI: http://doi.org/10.5808/GI.2017.15.1.38

Abstract

Research into new methods for identifying highly expressed genes in anonymous genome sequences has been going on for more than 15 years. We presented here an alternative approach based on modified score of relative codon usage bias to identify highly expressed genes in crenarchaeal genomes. The proposed algorithm relies exclusively on sequence features for identifying the highly expressed genes. In this study, a comparative analysis of predicted highly expressed genes in five crenarchaeal genomes was performed using the score of Modified Relative Codon Bias Strength (MRCBS) as a numerical estimator of gene expression level. We found a systematic strong correlation between Codon Adaptation Index and MRCBS. Additionally, MRCBS correlated well with other expression measures. Our study indicates that MRCBS can consistently capture the highly expressed genes.

Keyword

Archaea; Codon Adaptation Index; codon bias index; codon usage; GC content; gene expression; predicted highly expressed genes

MeSH Terms

Anonyms and Pseudonyms
Archaea
Base Composition
Bias (Epidemiology)
Codon
Gene Expression*
Genome*
Codon