ALGORITHMS AND SOFTWARE TOOLS FOR ORDERING CLONE LIBRARIES - APPLICATION TO THE MAPPING OF THE GENOME OF SCHIZOSACCHAROMYCES-POMBE
ALGORITHMS AND SOFTWARE TOOLS FOR ORDERING CLONE LIBRARIES - APPLICATION TO THE MAPPING OF THE GENOME OF SCHIZOSACCHAROMYCES-POMBE
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DOI：
10.1093/nar/21.8.1965
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发表时间：
1993-04-25
影响因子：
14.9
通讯作者：
LEHRACH, H
中科院分区：
文献类型：
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作者：
MOTT, R;GRIGORIEV, A;LEHRACH, H
一套完整的帮助基因组物理作图的软件工具已经开发出来，并成功应用于裂殖酵母裂殖酵母的基因组作图。有两种方法用于订购单拷贝杂交探针：一种是基于模拟退火算法来订购所有探针，另一种是使用启发式过滤程序推断探针的最小跨度子集。两种算法产生几乎相同的图谱，重复探针的顺序和具有相同杂交模式的探针的顺序略有差异。一个单独的算法使克隆符合既定的探针顺序。讨论了处理实验噪声和重复元素的方法。除了这些程序和数据库管理软件之外，还描述了用于可视化和编辑数据的工具。解决了组合来自不同图书馆的信息的问题。此外，还讨论了处理多拷贝探针和非杂交数据的方法。
A complete set of software tools to aid the physical mapping of a genome has been developed and successfully applied to the genomic mapping of the fission yeast Schizosaccharomyces pombe. Two approaches were used for ordering single-copy hybridisation probes: one was based on the simulated annealing algorithm to order all probes, and another on inferring the minimum-spanning subset of the probes using a heuristic filtering procedure. Both algorithms produced almost identical maps, with minor differences in the order of repetitive probes and those having identical hybridisation patterns. A separate algorithm fitted the clones to the established probe order. Approaches for handling experimental noise and repetitive elements are discussed. In addition to these programs and the database management software, tools for visualizing and editing the data are described. The issues of combining the information from different libraries are addressed. Also, ways of handling multiple-copy probes and non-hybridisation data are discussed.