OSLay: optimal syntenic layout of unfinished assemblies
OSLay: optimal syntenic layout of unfinished assemblies
复制标题
DOI：
10.1093/bioinformatics/btm153
复制
发表时间：
2007-07-01
期刊：
影响因子：
5.8
通讯作者：
Huson, Daniel H.
中科院分区：
文献类型：
--
作者：
Richter, Daniel C.;Schuster, Stephan C.;Huson, Daniel H.
全基因组鸟枪法进行基因组测序会产生一系列重叠群，这些重叠群必须进行排序和定向以促进有效的缺口闭合。我们提出了一种新的工具OSLay，该工具使用目标组装体和参考组装体中的匹配序列之间的同线性来布局目标组装体中的重叠群（或支架）。底层算法基于最大权重匹配。该工具提供了计算布局的交互式可视化，并且结果可以导入到组装编辑工具Consed中，以支持用于缺口闭合的引物对的设计。动机：为了提高基因组计划的差距闭合阶段的效率，了解靶基因组中哪些重叠群是相邻的是至关重要的。相关基因组序列可用于在组装中布置重叠群。
The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the contigs (or scaffolds) in the target assembly. The underlying algorithm is based on maximum weight matching. The tool provides an interactive visualization of the computed layout and the result can be imported into the assembly editing tool Consed to support the design of primer pairs for gap closure. Motivation: To enhance efficiency in the gap closure phase of a genome project it is crucial to know which contigs are adjacent in the target genome. Related genome sequences can be used to layout contigs in an assembly.