Algebraic correction methods for computational assessment of clone overlaps in DNA fingerprint mapping.
Algebraic correction methods for computational assessment of clone overlaps in DNA fingerprint mapping.
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DOI：
10.1186/1471-2105-8-127
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发表时间：
2007-04-18
影响因子：
3
通讯作者：
Wendl MC
中科院分区：
文献类型：
--
作者：
Wendl MC
Sulston评分是一个完善的，但近似的度量概率评估假设的克隆重叠的DNA指纹图谱。已知的是，系统地过度预测匹配概率的各种数量级，这取决于项目特定的参数。虽然精确的概率分布也可用于比较问题，但它相当难以计算，并且在大多数情况下不能直接使用。需要一种既能提高精度又能节省计算费用的方法。我们提出了一个简单的代数校正程序，它采取的Sulston分数作为一个临时值，并适用于幂律方程，以获得改进的结果。数值比较表明，显着增加的准确性，在传统的琼脂糖指纹图谱的典型参数的范围。还讨论了将该方法外推到较新的毛细管电泳项目的参数范围特征的问题。虽然计算成本仅略高于原始Sulston评分，但校正提供了对假设克隆重叠的极大改进的概率描述。这在重叠评估中显然是重要的，也许对其他任务也是重要的，例如在使用重叠概率的排序来帮助克隆排序时。
The Sulston score is a well-established, though approximate metric for probabilistically evaluating postulated clone overlaps in DNA fingerprint mapping. It is known to systematically over-predict match probabilities by various orders of magnitude, depending upon project-specific parameters. Although the exact probability distribution is also available for the comparison problem, it is rather difficult to compute and cannot be used directly in most cases. A methodology providing both improved accuracy and computational economy is required. We propose a straightforward algebraic correction procedure, which takes the Sulston score as a provisional value and applies a power-law equation to obtain an improved result. Numerical comparisons indicate dramatically increased accuracy over the range of parameters typical of traditional agarose fingerprint mapping. Issues with extrapolating the method into parameter ranges characteristic of newer capillary electrophoresis-based projects are also discussed. Although only marginally more expensive to compute than the raw Sulston score, the correction provides a vastly improved probabilistic description of hypothesized clone overlaps. This will clearly be important in overlap assessment and perhaps for other tasks as well, for example in using the ranking of overlap probabilities to assist in clone ordering.
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影响因子：
5.8
作者：
Flibotte, S;Chiu, R;Marra, MA
通讯作者：
Marra, MA
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Marra, MA
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