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

机译：FORS-D分析的评估：与统计上显着的茎环电位的比较

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摘要

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.
机译：核酸片段的茎环电位（以FONS值表示）分解为依赖于碱基组成的成分和依赖于碱基顺序的成分。后者表示为FORS-D值，是通过从FONS值中减去基本成分相关成分（FORS-M）的值得出的。 FORS-D分析是利用FORS-D值来估计潜在碱基顺序对茎环结构的贡献，并且已用于研究茎环结构与基因组其他选择压力之间的关系。在本研究中，我们通过将FORS-D分析与具有统计学意义的茎环潜力进行比较来评估FORS-D分析的可靠性，这是Le和Maizel开发的另一种健壮的方法，用于检查茎环结构。我们发现，使用10个随机序列计算出的FORS-M值与使用100个随机序列计算出的值一样可靠。所得的FORS-D值具有与统计上显着的茎环电位相似的趋势和分布，这意味着FORS-D分析在测量与基序相关的茎环电位的分布方面与后者一样可靠。由于FORS-M值的计算很耗时，因此我们开发的集成程序Bodslp将成为进行大规模FORS-D分析的便捷工具。结果还表明，出于某些目的，Le和Maizel开发的在线程序SigStb可以用作FORS-D分析的替代工具。

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