G-Anchor: a novel approach for whole-genome comparative mapping utilizing evolutionary conserved DNA sequences.
G-Anchor: a novel approach for whole-genome comparative mapping utilizing evolutionary conserved DNA sequences.
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DOI：
10.1093/gigascience/giy017
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发表时间：
2018-05-01
期刊：
影响因子：
9.2
通讯作者：
Larkin DM
中科院分区：
文献类型：
--
作者：
Lenis VPE;Swain M;Larkin DM
跨物种全基因组序列比对是基因组比较分析的关键第一步，范围从序列变异的检测到染色体进化的研究。动物基因组庞大而复杂，全基因组比对是一个计算密集的过程，由于需要探索广泛的局部比对，因此需要昂贵的高性能计算系统。随着来自多个项目的数百个已测序的动物基因组，对基因组比较分析的需求越来越大。在这里，我们介绍了G-锚，一个新的，快速，高效的管道，使用严格限制，但非常有效的一套本地序列比对锚（或地图）的动物基因组到另一个物种的参考基因组。G-Anchor对高度保守的DNA序列元件的数据库进行了新的利用。我们展示了这些元素如何与一对基因组对齐，从而创建锚。这些锚使得支架能够从从头组装的基因组快速映射到参考物种的染色体组装。我们的研究结果表明，G-锚可以成功地锚脊椎动物基因组上的遗传相关的参考物种的基因组，使用台式或笔记本电脑在几个小时内，并具有可比的准确性，实现了一个高度准确的全基因组比对工具，如LASTZ。因此，G-Anchor使计算资源有限的研究人员可以进行全基因组比较。G-Anchor是一种用于锚定一对脊椎动物基因组的现成工具。它可以用于包含进化保守DNA序列的显著部分并且不是高度重复、息肉状或过度片段化的大基因组。G-Anchor不是全基因组比对软件的替代品，但可用于快速准确的初始基因组比较。G-Anchor是免费提供的，是一种随时可用的工具，用于两个基因组的成对比较。
Cross-species whole-genome sequence alignment is a critical first step for genome comparative analyses, ranging from the detection of sequence variants to studies of chromosome evolution. Animal genomes are large and complex, and whole-genome alignment is a computationally intense process, requiring expensive high-performance computing systems due to the need to explore extensive local alignments. With hundreds of sequenced animal genomes available from multiple projects, there is an increasing demand for genome comparative analyses. Here, we introduce G-Anchor, a new, fast, and efficient pipeline that uses a strictly limited but highly effective set of local sequence alignments to anchor (or map) an animal genome to another species’ reference genome. G-Anchor makes novel use of a databank of highly conserved DNA sequence elements. We demonstrate how these elements may be aligned to a pair of genomes, creating anchors. These anchors enable the rapid mapping of scaffolds from a de novo assembled genome to chromosome assemblies of a reference species. Our results demonstrate that G-Anchor can successfully anchor a vertebrate genome onto a phylogenetically related reference species genome using a desktop or laptop computer within a few hours and with comparable accuracy to that achieved by a highly accurate whole-genome alignment tool such as LASTZ. G-Anchor thus makes whole-genome comparisons accessible to researchers with limited computational resources. G-Anchor is a ready-to-use tool for anchoring a pair of vertebrate genomes. It may be used with large genomes that contain a significant fraction of evolutionally conserved DNA sequences and that are not highly repetitive, polypoid, or excessively fragmented. G-Anchor is not a substitute for whole-genome aligning software but can be used for fast and accurate initial genome comparisons. G-Anchor is freely available and a ready-to-use tool for the pairwise comparison of two genomes.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
4.1
作者：
Ekblom R;Wolf JB
通讯作者：
Wolf JB
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
影响因子：
14.9
作者：
Stojanovic, N;Florea, L;Hardison, R
通讯作者：
Hardison, R
影响因子：
7
作者：
Siepel, A;Bejerano, G;Haussler, D
通讯作者：
Haussler, D