Semi-Automated Method for Annotating Repeated Sequences

注释重复序列的半自动方法

• 批准号: 6701910
• 负责人: MITRICK A JOHNS
• 金额: $ 21.47万
• 依托单位: NORTHERN ILLINOIS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-02-01 至 2008-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6701910
• 关键词: Arabidopsis; biomedical automation; biotechnology; functional /structural genomics; high throughput technology; molecular biology information system; nucleic acid repetitive sequence; nucleic acid sequence; plant genetics; rice

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.

这个项目开发了一个图形化的方法来识别和注释染色体长度的DNA序列组装上发现的重复序列。重复序列包括转座因子、复制基因、细胞器插入和其他结构。特别是已知转座因子插入基因中，引起基因突变和体细胞突变，包括癌症。这里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。然后将结果显示在“BLAST点图”上，其中X和y轴均表示染色体的部分。x轴以每像素30个碱基对的分辨率显示，这一分辨率使得几乎所有的基因和转座因子都能轻松地显示在一个计算机屏幕上。y轴以50，000 bp/像素显示，这允许整个染色体显示在单个屏幕上。重复序列很容易被看作是一系列堆叠的水平线，其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连同从其它搜索软件得到的附加信息一起沿着输入数据库。此外，有关家庭相关性和结构相似性的信息可以超链接到显示。