Genotator: A workbench for sequence annotation
Genotator: A workbench for sequence annotation
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DOI：
10.1101/gr.7.7.754
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发表时间：
1997-07-01
期刊：
影响因子：
7
通讯作者：
Harris, NL
中科院分区：
文献类型：
--
作者：
Harris, NL
测序中心，如LBNL的人类基因组中心，正在产生越来越多的遗传数据。注释可以大大提高这些序列的生物学价值。有用的注释包括可能的基因位置、与已知基因的同源性和基因信号，如启动子和剪接位点。Genotator是一个用于自动序列注释和注释浏览的工作台。后端在DNA序列上运行一系列序列分析工具，处理工具所需的各种输入和输出格式。Genotator目前运行五个不同的基因发现程序，三个同源性搜索，并搜索启动子，剪接位点和ORF。可以通过交互式图形浏览器查看Genotator运行的分析结果。浏览器在画布上显示颜色编码的序列注释，可以滚动和缩放，允许在多个细节级别上探索注释的序列。用户可以在单独的窗口中查看实际的DNA序列;当在图谱显示中选择一个区域时，该区域将在序列显示中自动突出显示，反之亦然。通过显示所有序列分析的输出，Genotator提供了一种直观的方法来识别序列中的重要区域（例如，可能的外显子）。用户可以交互式地添加个人注释来标记感兴趣的区域。Genotator的其他功能包括引物设计和模式搜索。
Sequencing centers such as the Human Genome Center at LBNL are producing an ever-increasing flood of genetic data. Annotation can greatly enhance the biological value of these sequences. Useful annotations include possible gene locations, homologies to known genes, and gene signals such as promoters and splice sites. Genotator is a workbench for automated sequence annotation and annotation browsing. The back end runs a series of sequence analysis tools on a DNA sequence, handling the various input and output formats required by the tools. Genotator currently runs five different gene-finding programs, three homology searches, and searches for promoters, splice sites, and ORFs. The results of the analyses run by Genotator can be viewed with the interactive graphical browser. The browser displays color-coded sequence annotations on a canvas that carl be scrolled and zoomed, allowing the annotated sequence to be explored at multiple levels of detail. The user can view the actual DNA sequence in a separate window; when a region is selected in the map display, it is highlighted automatically in the sequence display, and vice versa. By displaying the output of all of the sequence analyses, Genotator provides an intuitive way to identify the significant regions (for example, probable exons) in a sequence. Users can interactively add personal annotations to label regions of interest. Additional capabilities of Genotator include primer design and pattern searching.