Barcode server: a visualization-based genome analysis system.
Barcode server: a visualization-based genome analysis system.
复制标题
DOI：
10.1371/journal.pone.0056726
复制
发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Xu Y
中科院分区：
文献类型：
--
作者：
Mao F;Olman V;Wang Y;Xu Y
我们以前已经开发了一种计算方法，用于将基因组表示为条形码图像，这使得各种基因组特征在视觉上明显。我们已经证明，这种视觉能力使一些具有挑战性的基因组分析问题相对容易解决。我们已将这种能力应用于许多具有挑战性的问题，包括（a）水平转移基因的识别，（B）具有特殊性质的基因组岛的识别和（c）宏基因组序列的分箱，并取得了非常令人鼓舞的结果。这些应用结果启发我们开发这种用于公共服务的基于条形码的基因组分析服务器，其支持以下能力：（a）计算所提供的DNA序列的基于k-mer的条形码图像;（B）检测给定基因组中具有不同于大多数基因组的条形码的序列片段;（c）将所提供的DNA序列聚类成具有相似条形码的组;和（d）使用Blast对基因组数据库进行基于同源性的搜索，以寻找被认为具有感兴趣的条形码的任何选定的基因组区域。条形码服务器提供作业管理功能，允许处理大量分析作业，用于基于条形码的比较基因组分析。条形码服务器可通过http://csbl1.bmb.uga.edu/Barcode访问。
We have previously developed a computational method for representing a genome as a barcode image, which makes various genomic features visually apparent. We have demonstrated that this visual capability has made some challenging genome analysis problems relatively easy to solve. We have applied this capability to a number of challenging problems, including (a) identification of horizontally transferred genes, (b) identification of genomic islands with special properties and (c) binning of metagenomic sequences, and achieved highly encouraging results. These application results inspired us to develop this barcode-based genome analysis server for public service, which supports the following capabilities: (a) calculation of the k-mer based barcode image for a provided DNA sequence; (b) detection of sequence fragments in a given genome with distinct barcodes from those of the majority of the genome, (c) clustering of provided DNA sequences into groups having similar barcodes; and (d) homology-based search using Blast against a genome database for any selected genomic regions deemed to have interesting barcodes. The barcode server provides a job management capability, allowing processing of a large number of analysis jobs for barcode-based comparative genome analyses. The barcode server is accessible at http://csbl1.bmb.uga.edu/Barcode.
影响因子：
3
作者：
Zhou, Fengfeng;Olman, Victor;Xu, Ying
通讯作者：
Xu, Ying
使用基因组条形码预测肠出血性大肠杆菌 O157:H7 的致病岛
影响因子：
3.5
作者：
Wang, Guoqing;Zhou, Fengfeng;Xu, Ying
通讯作者：
Xu, Ying
影响因子：
14.9
作者：
Tsirigos A;Rigoutsos I
通讯作者：
Rigoutsos I