Siegel A F, Roach J C, Magness C, Thayer E, van den Engh G
Department of Management Science, University of Washington, Seattle, WA 98195, USA.
J Comput Biol. 1998 Spring;5(1):113-26. doi: 10.1089/cmb.1998.5.113.
Consider a mapping project in which overlap of clonal segments is inferred from complete multiple restriction digests. The fragment sizes of the clones are measured with some error, potentially leading to a map with erroneous links. The number of errors in the map depends on the number and types of enzymes used to characterize the clones. The most critical parameter is the decision rule k, or the criterion for declaring clone overlap. Small changes in k may cause an order of magnitude change in the amount of work it takes to build a map of given completion. We observe that the cost of an optimal mapping strategy is approximately proportional to the target size. While this finding is encouraging, considerable effort is nonetheless required: for large-scale sequencing projects with up-front mapping, mapping will be a non-negligible fraction of the total sequencing cost.
考虑一个映射项目，其中克隆片段的重叠是从完整的多重限制性酶切分析中推断出来的。克隆片段的大小测量存在一定误差，这可能导致构建出带有错误连接的图谱。图谱中的错误数量取决于用于表征克隆的酶的数量和类型。最关键的参数是决策规则k，即声明克隆重叠的标准。k的微小变化可能会使构建给定完整度图谱所需的工作量发生一个数量级的变化。我们观察到，最优映射策略的成本大致与目标大小成正比。虽然这一发现令人鼓舞，但仍需要付出相当大的努力：对于前期需要进行映射的大规模测序项目，映射将占总测序成本中不可忽视的一部分。
