Sonnhammer E L, Durbin R
Sanger Centre, Hinxton Hall, Cambridge, UK.
Gene. 1995 Dec 29;167(1-2):GC1-10. doi: 10.1016/0378-1119(95)00714-8.
Graphical dot-matrix plots can provide the most complete and detailed comparison of two sequences. Presented here is DOTTER2, a dot-plot program for X-windows which can compare DNA or protein sequences, and also DNA versus protein. The main novel feature of DOTTER is that the user can vary the stringency cutoffs interactively, so that the dot-matrix only needs to be calculated once. This is possible thanks to a 'Greyramp tool' that was developed to change the displayed stringency of the matrix by dynamically changing the greyscale rendering of the dots. The Greyramp tool allows the user to interactively change the lower and upper score limit for the greyscale rendering. This allows exploration of the separation between signal and noise, and fine-grained visualisation of different score levels in the dot-matrix. Other useful features are dot-matrix compression, mouse-controlled zooming, sequence alignment display and saving/loading of dot-matrices. Since the matrix only has to be calculated once and since the algorithm is fast and linear in space, DOTTER is practical to use even for sequences as long as cosmids. DOTTER was integrated in the gene-modelling module of the genomic database system ACEDB3. This was done via the homology viewer BLIXEM in a way that also allows segments from the BLAST suite of searching programs to be superimposed on top of the full dot-matrix. This feature can also be used for very quick finding of the strongest matches. As examples, we analyse a Caenorhabditis elegans cosmid with several tandem repeat families, and illustrate how DOTTER can improve gene modelling.
图形点阵图可以对两个序列进行最完整、最详细的比较。这里介绍的是DOTTER2，一个用于X窗口的点阵程序，它可以比较DNA或蛋白质序列，也可以比较DNA与蛋白质。DOTTER的主要新颖之处在于用户可以交互式地改变严格性阈值，这样点阵只需要计算一次。这要归功于一个“灰度渐变工具”，它通过动态改变点的灰度渲染来改变矩阵显示的严格性。灰度渐变工具允许用户交互式地改变灰度渲染的下限和上限分数限制。这有助于探索信号与噪声之间的分离，并对点阵中不同分数水平进行细粒度可视化。其他有用的功能包括点阵压缩、鼠标控制缩放、序列比对显示以及点阵的保存/加载。由于矩阵只需要计算一次，而且算法速度快且空间线性，即使对于长达黏粒的序列，DOTTER也很实用。DOTTER被集成到基因组数据库系统ACEDB3的基因建模模块中。这是通过同源性查看器BLIXEM完成的，其方式还允许来自BLAST搜索程序套件的片段叠加在完整的点阵之上。此功能也可用于非常快速地找到最强匹配项。作为示例，我们分析了一个带有几个串联重复家族的秀丽隐杆线虫黏粒，并说明了DOTTER如何改进基因建模。
