A rebuttal to the comments on the genome order index and the Z-curve
2011
Rebuttal on Genome Order Index and Z-Curve
Sample size: 235
Commentary
Evidence: moderate
Author Information
Author(s): Zhang Ren
Primary Institution: Department of Epidemiology and Biostatistics, Tianjin Cancer Institute and Hospital, Tianjin, PR China
Conclusion
The criticisms of Elhaik, Graur, and Josic regarding the genome order index and Z-curve are incorrect.
Supporting Evidence
- Elhaik et al. made errors in calculating the radius of the inscribed sphere.
- The exponential distribution of S is a restatement of previous conclusions.
- Elhaik et al. incorrectly treated deviations from Chargaff's second parity rule as zero.
- Biological significance should not be dismissed based on numerical smallness.
Takeaway
This study argues that previous criticisms of a method for analyzing DNA sequences are wrong and that the method is still valid.
Methodology
The study analyzed the same 235 bacterial genomes used by Elhaik et al. to rebut their claims.
Limitations
The rebuttal is based on the same data set, which may not represent all genomes.
Participant Demographics
The study focused on 235 bacterial genomes.
Digital Object Identifier (DOI)
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