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Evaluation of FORS-D Analysis: A Comparison with the Statistically Significant Stem-loop Potential

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Abstract

The stem-loop potential of a nucleic acid segment (expressed as a FONS value), decomposes into base composition-dependent and base order-dependent components. The latter, expressed as a FORS-D value, is derived by subtracting the value of the base composition-dependent component (FORS-M) from the FONS value. FORS-D analysis is the use of FORS-D values to estimate the potential of local base order to contribute to a stem-loop structure, and it has been used to investigate the relationship between stem-loop structure and other selective pressures on genomes. In the present study, we evaluated the reliability of FORS-D analysis by comparing it with statistically significant stem-loop potential, another robust method developed by Le and Maizel for examining stem-loop structure. We found that FORS-M values calculated using 10 randomized sequences are as reliable as those calculated using 100 randomized sequences. The resulting FORS-D values have a similar trend and distribution as statistically significant stem-loop potential, implying that FORS-D analysis is as reliable as the latter in measuring the distribution of base order-dependent stem-loop potential. Since the calculation of the FORS-M values is time consuming, the integrated program Bodslp developed by us will become a convenient tool for large-scale FORS-D analysis. The results also suggest that for some purposes the online program SigStb developed by Le and Maizel may be used as an alternative tool for FORS-D analysis.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (No. 30600352), the Natural Science Foundation of Jiangsu Province, China (No. BK2006550), the Startup Fund from Jiangsu University for Advanced Scholars (No. 2281270002), the Startup Fund of First Affiliated Hospital of Nanjing Medical University for Advanced Scholars, and the Startup Fund for Zhenjiang Key Institute of Clinical Laboratory Science (No. SH2006066).

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, Jiangsu University School of Medical Technology, Zhenjiang, Jiangsu, 212001, P.R. China

    Chi-Yu Zhang

  2. First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210026, P.R. China

    Ji-Fu Wei & Shao-Heng He

  3. State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096, P.R. China

    Jian-Sheng Wu & Xiao Sun

  4. Zhenjiang Key Institute of Clinical Laboratory Science, Zhenjiang, Jiangsu, 212001, P.R. China

    Wen-Rong Xu

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  1. Chi-Yu Zhang
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  2. Ji-Fu Wei
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  3. Jian-Sheng Wu
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  4. Wen-Rong Xu
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  5. Xiao Sun
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  6. Shao-Heng He
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Corresponding author

Correspondence to Shao-Heng He.

Additional information

C. Y. Zhang and J. F. Wei contributed equally to this paper.

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Zhang, CY., Wei, JF., Wu, JS. et al. Evaluation of FORS-D Analysis: A Comparison with the Statistically Significant Stem-loop Potential. Biochem Genet 46, 29–40 (2008). https://doi.org/10.1007/s10528-007-9126-6

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  • DOI: https://doi.org/10.1007/s10528-007-9126-6

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