PAIRWISE END SEQUENCING - A UNIFIED APPROACH TO GENOMIC MAPPING AND SEQUENCING
PAIRWISE END SEQUENCING - A UNIFIED APPROACH TO GENOMIC MAPPING AND SEQUENCING
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DOI：
10.1016/0888-7543(95)80219-c
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发表时间：
1995-03-20
期刊：
影响因子：
4.4
通讯作者：
HOOD, L
中科院分区：
文献类型：
--
作者：
ROACH, JC;BOYSEN, C;HOOD, L
目前大规模基因组 DNA 测序的策略需要进行物理作图，然后进行详细作图，最后进行测序。映射的详细程度决定了完成项目所需的工作量或顺序冗余。当前的策略试图在绘图和测序工作之间找到平衡。一种这样的方法是采用使用序列数据来构建物理图的策略。这样的映射减轻了对先前映射的需要并减少了最终所需的序列冗余。为此，人们充分认识到关联源自亚克隆模板两端的序列数据对的效用。然而，尚未建立采用此类成对数据的最佳策略。在目前的工作中，我们模拟并分析了成对测序项目的参数，包括模板长度、序列读长和总序列冗余度。推荐一种基于对质粒亚克隆两端进行测序的成对策略，并通过原始数据模拟进行说明。我们发现成对策略对小（cosmid）和大（megaYAC）目标均有效，并产生具有高度映射完整性的有序序列数据。它们是精细绘图和基因查找的理想选择，也是高冗余或低冗余测序工作的初始步骤。这种策略是高度自动化的。 (C) 1995 学术出版社
Strategies for large-scale genomic DNA sequencing currently require physical mapping, followed by detailed mapping, and finally sequencing. The level of mapping detail determines the amount of effort, or sequence redundancy, required to finish a project. Current strategies attempt to find a balance between mapping and sequencing efforts. One such approach is to employ strategies that use sequence data to build physical maps. Such maps alleviate the need for prior mapping and reduce the final required sequence redundancy. To this end, the utility of correlating pairs of sequence data derived from both ends of subcloned templates is well recognized. However, optimal strategies employing such pairwise data have not been established. In the present work, we simulate and analyze the parameters of pairwise sequencing projects including template length, sequence read length, and total sequence redundancy. One pairwise strategy based on sequencing both ends of plasmid subclones is recommended and illustrated with raw data simulations. We find that pairwise strategies are effective with both small (cosmid) and large (megaYAC) targets and produce ordered sequence data with a high level of mapping completeness. They are ideal for fine-scale mapping and gene finding and as initial steps for either a high- or a low-redundancy sequencing effort. Such strategies are highly automatable. (C) 1995 Academic Press, Inc.