Strategies and tools for whole-genome alignments
Strategies and tools for whole-genome alignments
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DOI：
10.1101/gr.762503
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发表时间：
2003-01-01
期刊：
影响因子：
7
通讯作者：
Dubchak, I
中科院分区：
文献类型：
--
作者：
Couronne, O;Poliakov, A;Dubchak, I
小鼠基因组的组装首次使两种大型脊椎动物基因组的所有比对和比较成为可能。我们研究了不同的比对策略，用于随后的基因组保守性分析，这些策略对不同质量的组装有效。将这些策略应用于人类基因组工作草图与小鼠基因组测序联盟组装体以及其他中间小鼠组装体的比较。我们的方法是快速的，所得到的比对表现出高度的灵敏度，覆盖了人类基因组中90%以上的已知编码外显子。我们在保持特异性的同时获得了这样的覆盖率。鉴于瓷砖最终用户，我们开发了一套工具和网站自动对齐，随后浏览和工作与全基因组比较。我们描述了使用这些工具来识别人类和小鼠基因组之间的保守非编码区，其中一些尚未通过其他方法识别。
The availability of the assembled mouse genome makes possible, for tile first time, all alignment and comparison of two large vertebrate genomes. We investigated different strategies of alignment for tile subsequent analysis of conservation of genomes that are effective for assemblies of different quality. These strategies were applied to the comparison of the working draft of tile human genome with tile Mouse Genome Sequencing Consortium assembly, as well as other intermediate mouse assemblies. Our methods are fast and the resulting alignments exhibit a high degree of sensitivity, covering more than 90% of known coding exons in the human genome. We obtained such coverage while preserving specificity. With a view towards tile end user, we developed a suite of tools and Web sites for automatically aligning and subsequently browsing and working with whole-genome comparisons. We describe the use of these tools to identify conserved non-coding regions between tile human and mouse genomes, some of which have not been identified by other methods.