Semi-Automated Method for Annotating Repeated Sequences

这个项目开发了一种图形化的方法来识别和注释在染色体长度的DNA序列组合上发现的重复序列。重复序列包括转座元件、重复基因、细胞器插入和其他结构。特别是已知转座子插入基因，导致生发突变和包括癌症在内的体细胞突变。这里正在开发的基本方法使用针对整个染色体序列的染色体片段的BLAST搜索。然后，结果会显示在“BLAST点图”上，其中x轴和y轴都代表染色体的各个部分。X轴以每像素30个碱基对的速度显示，这一分辨率使几乎所有基因和转座元件都能轻松地显示在一个计算机屏幕上。Y轴以50000个/像素的速度显示，这使得整个染色体可以显示在一个屏幕上。重复序列很容易被视为一系列堆叠的水平线，它们的位置和颜色显示了每个重复的染色体位置和相似性。每个重复的坐标可以与从其他搜索软件获得的附加信息一起输入到数据库中。此外，关于家庭亲缘关系和结构相似性的信息可以超链接到显示。

This project develops a graphical method for identifying and annotating repeated sequences found on chromosome-length DNA sequence assemblies. Repeated sequences include transposable elements, duplicated genes, organellar insertions, and other structures. Transposable elements in particular are known to insert into genes, causing both germinal mutations and somatic mutations including cancer. The basic method being developed here uses a BLAST search of segments of the chromosome against the entire chromosome sequence. The results are then displayed on a "BLAST dotplot", where both the x and y axes represent sections of the chromosome. The x-axis is displayed at 30 base pairs per pixel, a resolution that allows almost all genes and transposable elements to easily fit on a single computer screen. The y-axis is displayed at 50,000 bp/pixel, which allows the entire chromosome to be displayed on a single screen. Repeated sequences are easily seen as a series of stacked horizontal lines whose position and color shows the chromosomal location and similarity of each repeat. The coordinates of each repeat can be entered into a database along with additional information derived from other search software. Also, information about family relatedness and structural similarity can be hyperlinked to the display.