Comparative Analysis of Predicted Gene Expression among Crenarchaeal Genomes
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 prop...
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BioMed Central
2017-03-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gni-15-38.pdf |
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| author | Shibsankar Das Brajadulal Chottopadhyay Satyabrata Sahoo |
| author_facet | Shibsankar Das Brajadulal Chottopadhyay Satyabrata Sahoo |
| author_sort | Shibsankar Das |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-4b835ad872404303a126d1df7082f5a3 |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2017-03-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-4b835ad872404303a126d1df7082f5a32025-02-02T15:39:34ZengBioMed CentralGenomics & Informatics1598-866X2234-07422017-03-01151384710.5808/GI.2017.15.1.38204Comparative Analysis of Predicted Gene Expression among Crenarchaeal GenomesShibsankar Das0Brajadulal Chottopadhyay1Satyabrata Sahoo2Department of Mathematics, Uluberia College, Uluberia 711315, India.Department of Physics, Jadavpur University, Kolkata 700032, India.Dhruba Chand Halder College, South 24 Parganas 743372, India.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.http://genominfo.org/upload/pdf/gni-15-38.pdfArchaeaCodon Adaptation Indexcodon bias indexcodon usageGC contentgene expressionpredicted highly expressed genes |
| spellingShingle | Shibsankar Das Brajadulal Chottopadhyay Satyabrata Sahoo Comparative Analysis of Predicted Gene Expression among Crenarchaeal Genomes Genomics & Informatics Archaea Codon Adaptation Index codon bias index codon usage GC content gene expression predicted highly expressed genes |
| title | Comparative Analysis of Predicted Gene Expression among Crenarchaeal Genomes |
| title_full | Comparative Analysis of Predicted Gene Expression among Crenarchaeal Genomes |
| title_fullStr | Comparative Analysis of Predicted Gene Expression among Crenarchaeal Genomes |
| title_full_unstemmed | Comparative Analysis of Predicted Gene Expression among Crenarchaeal Genomes |
| title_short | Comparative Analysis of Predicted Gene Expression among Crenarchaeal Genomes |
| title_sort | comparative analysis of predicted gene expression among crenarchaeal genomes |
| topic | Archaea Codon Adaptation Index codon bias index codon usage GC content gene expression predicted highly expressed genes |
| url | http://genominfo.org/upload/pdf/gni-15-38.pdf |
| work_keys_str_mv | AT shibsankardas comparativeanalysisofpredictedgeneexpressionamongcrenarchaealgenomes AT brajadulalchottopadhyay comparativeanalysisofpredictedgeneexpressionamongcrenarchaealgenomes AT satyabratasahoo comparativeanalysisofpredictedgeneexpressionamongcrenarchaealgenomes |