Limitations of codon adaptation index and other coding DNA-based features for prediction of protein expression inSaccharomyces cerevisiae

Yeast ◽  
2004 ◽  
Vol 21 (13) ◽  
pp. 1083-1093 ◽  
Author(s):  
Markus Friberg ◽  
Peter von Rohr ◽  
Gaston Gonnet
Keyword(s):  
Protein Expression ◽  
Codon Adaptation Index ◽  
Adaptation Index

scholarly journals Codon adaptation index as a measure of dominating codon bias

2003 ◽  
Vol 19 (16) ◽  
pp. 2005-2015 ◽  
Author(s):  
A. Carbone ◽  
A. Zinovyev ◽  
F. Kepes
Keyword(s):  
Codon Bias ◽  
Codon Adaptation Index ◽  
Adaptation Index

scholarly journals Relative Codon Adaptation Index, a Sensitive Measure of Codon Usage Bias

2010 ◽  
Vol 6 ◽  
pp. EBO.S4608 ◽  
Author(s):  
Soohyun Lee ◽  
Seyeon Weon ◽  
Sooncheol Lee ◽  
Changwon Kang
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Codon Adaptation Index ◽  
Sensitive Measure ◽  
Adaptation Index

scholarly journals E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI)

2008 ◽  
Vol 9 (1) ◽  
pp. 65 ◽  
Author(s):  
Pere Puigbò ◽  
Ignacio G Bravo ◽  
Santiago Garcia-Vallvé
Keyword(s):  
Expected Value ◽  
Codon Adaptation Index ◽  
Adaptation Index

scholarly journals A New Look at Codon Usage and Protein Expression

10.29007/d4tz ◽  
2019 ◽  
Author(s):  
Gabriel Wright ◽  
Anabel Rodriguez ◽  
Patricia Clark ◽  
Scott Emrich
Keyword(s):  
Protein Expression ◽  
Codon Usage ◽  
Empirical Data ◽  
Codon Usage Bias ◽  
Elongation Rate ◽  
Translation Rate ◽  
Translation Elongation ◽  
Promising Alternative ◽  
Highly Expressed Genes ◽  
Adaptation Index

%MinMax, a model of intra-gene translational elongation rate, relies on codon usage frequencies. Historically, %MinMax has used tables that measure codon usage bias for all genes in an organism, such as those found at HIVE-CUT. In this paper, we provide evidence that codon usage bias based on all genes is insufficient to accurately measure absolute translation rate. We show that alternative ”High-φ” codon usage tables, generated by another model (ROC-SEMPPR), are a promising alternative. By creating a hybrid model, future codon usage analyses and their applications (e.g., codon harmonization) are likely to more accurately measure the ”tempo” of translation elongation. We also suggest a High- φ alternative to the Codon Adaptation Index (CAI), a classic metric of codon usage bias based on highly expressed genes. Significantly, our new alternative is equally well correlated with empirical data as traditional CAI without using experimentally determined expression counts as input.

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