Contigs built with fingerprints, markers, and FPCV4.7
Contigs built with fingerprints, markers, and FPCV4.7
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DOI：
10.1101/gr.gr-1375r
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发表时间：
2000-11-01
期刊：
影响因子：
7
通讯作者：
French, L
中科院分区：
文献类型：
--
作者：
Soderlund, C;Humphray, S;French, L
重叠群已经组装，并且选择了超过2800个克隆用于人类染色体9、10和13的测序。使用FPC（FingerPrinted Contig）软件，重叠群与标记和完整的消化指纹组装，并且重叠群通过全局框架排序和定位。已使用公开可用的资源，例如1998年国际基因图谱的框架和GSC人类PAC指纹数据库的大多数指纹。在内部生成额外的标记和指纹，以补充这些数据。为了支持构建图的放大，FPC V4.7已经扩展到使用具有指纹的标记来组装重叠群，新的克隆和标记可以自动添加到现有的重叠群，并且相应地标记组装不良的重叠群。为了测试自动组装，使用110 Mb串联人类序列的模拟完整摘要来创建具有不同覆盖度、克隆长度和错误类型的数据集。当没有引入错误并且在组装中使用公差7时，没有假阳性重叠的最大重叠群具有9534个克隆和32个无序克隆，即，相邻克隆的起始坐标处于错误的顺序。本文描述了FPC中的新功能，构建染色体9，10和13的图谱的场景，以及模拟的结果。
Contigs have been assembled, and over 2800 clones selected for sequencing for human chromosomes 9, 10 and 13. Using the FPC (FingerPrinted Contig) software, the contigs are assembled with markers and complete digest fingerprints, and the contigs are ordered and localised by a global Framework. Publicly available resources have been used, such as, the 1998 International Gene Map for the framework and the GSC Human PAC fingerprint database for the majority of the fingerprints. Additional markers and fingerprints are generated in-house to supplement this data. To support the scale up of building maps, FPC V4.7 has been extended to use markers with the fingerprints for assembly of contigs, new clones and markers can be automatically added to existing contigs, and poorly assembled contigs are marked accordingly. To test the automatic assembly, a simulated complete digest of 110 Mb of concatenated human sequence was used to create datasets with varying coverage, length of clones, and types of error. When no error was introduced and a tolerance of 7 was used in assembly, the largest contig with no false positive overlaps has 9534 clones with 32 out-of-order clones, that is, the starting coordinates of adjacent clones are in the wrong order. This paper describes the new Features in FPC, the scenario for building the maps of chromosomes 9, 10 and 13, and the results From the simulation.