EDGAR: a software framework for the comparative analysis of prokaryotic genomes.
EDGAR: a software framework for the comparative analysis of prokaryotic genomes.
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DOI：
10.1186/1471-2105-10-154
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发表时间：
2009-05-20
影响因子：
3
通讯作者：
Goesmann A
中科院分区：
文献类型：
--
作者：
Blom J;Albaum SP;Doppmeier D;Pühler A;Vorhölter FJ;Zakrzewski M;Goesmann A
下一代测序方法的引入导致了完全测序的基因组数量的快速增加。作为这一发展的结果之一，现在可以用比较方法分析大量相关基因组。比较基因组学的一个主要任务是鉴定不同基因组中的直向同源基因，并将基因分类为核心基因或单基因。为了支持这些研究，开发了EDGAR -“使用BLAST评分比进行比较基因组分析的有效数据库框架”。埃德加旨在以高通量方法自动执行基因组比较。利用该软件对NCBI基因组数据库中75个属组的582个基因组进行了比较分析，并将结果整合到基础数据库中。为了证明一个具体的应用情况下，我们分析了细菌属黄单胞菌，系统发育研究是尴尬的，由于不同的分类系统的10个基因组。埃德加提供的结果与最近进行的传统方法的结果一致，此外，可以以前所未有的准确性确定每种菌株的根。埃德加提供了新的分析功能，并大大简化了相关基因组的比较分析。该软件支持对进化关系的快速调查，并简化了获得有关亲缘基因组差异基因内容的新生物学见解的过程。可视化功能，如同线图或维恩图，提供给科学界通过一个基于网络的，因此平台独立的用户界面，其中预先计算的数据集可以浏览。
The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. To support these studies EDGAR – "Efficient Database framework for comparative Genome Analyses using BLAST score Ratios" – was developed. EDGAR is designed to automatically perform genome comparisons in a high throughput approach. Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database. To demonstrate a specific application case, we analyzed ten genomes of the bacterial genus Xanthomonas, for which phylogenetic studies were awkward due to divergent taxonomic systems. The resultant phylogeny EDGAR provided was consistent with outcomes from traditional approaches performed recently and moreover, it was possible to root each strain with unprecedented accuracy. EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes. The software supports a quick survey of evolutionary relationships and simplifies the process of obtaining new biological insights into the differential gene content of kindred genomes. Visualization features, like synteny plots or Venn diagrams, are offered to the scientific community through a web-based and therefore platform independent user interface , where the precomputed data sets can be browsed.
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影响因子：
4.3
作者：
Altenhoff, Adrian M.;Dessimoz, Christophe
通讯作者：
Dessimoz, Christophe
DOI：
10.2307/2412448
发表时间：
1970-01-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
FITCH, WM
通讯作者：
FITCH, WM
影响因子：
5.8
作者：
Ciria, R;Abreu-Goodger, C;Merino, E
通讯作者：
Merino, E
影响因子：
14.9
作者：
Frazer, KA;Pachter, L;Dubchak, I
通讯作者：
Dubchak, I
影响因子：
14.9
作者：
Chaudhuri RR;Pallen MJ
通讯作者：
Pallen MJ