MGView: an alignment and visualization tool to enhance gap closure of microbial genomes
MGView: an alignment and visualization tool to enhance gap closure of microbial genomes
复制标题
DOI：
10.1093/nar/gng107
复制
发表时间：
2003-09-01
影响因子：
14.9
通讯作者：
Kapur, V
中科院分区：
文献类型：
--
作者：
Herron-Olson, L;Freeman, J;Kapur, V
在微生物随机散弹枪基因组测序项目中，缝隙关闭是一个具有挑战性的阶段，特别是因为基因组组装往往由于重复元件、插入序列和其他导致序列错误组装的类似因素的存在而变得复杂。虽然众所周知，微生物基因组之间遗传信息的保存，加上可用微生物序列的指数增长，可以用来提高缝合缺口的效率，但我们缺乏帮助这一过程的计算工具。我们在这里描述了一个新的工具，MGView，它是为了创建一组微生物重叠群与完整微生物基因组的比对的图形描述而开发的。我们组装金黄色葡萄球菌RF122基因组的结果表明，MGView能够显著减少与关闭相关的时间和经济成本。总之，结果还表明，MGView的应用不仅能够减少随机猎枪序列阶段的折叠覆盖要求，而且还提供了对已完成和未完成的微生物基因组之间的基因内容和组织差异的有趣见解。
Gap closure is a challenging phase in microbial random shotgun genome sequencing projects, particularly since genome assemblies are often complicated by the presence of repeat elements, insertion sequences and other similar factors that contribute to sequence misassemblies. While it is well recognized that the conservation of genetic information between microbial genomes, combined with the exponential increase in available microbial sequences, can be exploited to increase the efficiency of gap closure, we lack the computational tools to aid in this process. We describe here a new tool, MGView, which was developed to create a graphical depiction of the alignment of a set of microbial contigs against a completed microbial genome. The results of our assembly of the Staphylococcus aureus RF122 genome show that MGView enables a considerable reduction in time and economic cost associated with closure. Together, the results also show that the application of MGView not only enables a reduction in fold-coverage requirements of the random shotgun sequence phase, but also provides interesting insights into differences in gene content and organization between finished and unfinished microbial genomes.