Yang Long, Jin Gulei, Zhao Xiangqian, Zheng Yan, Xu Zhaohua, Wu Weiren
Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, China.
Bioinformatics. 2007 Aug 15;23(16):2174-7. doi: 10.1093/bioinformatics/btm296. Epub 2007 Jun 1.
With the recent progress made in large-scale plant functional genome sequencing projects, a great amount of EST (express sequence tag) data is becoming available. With the help of complete genomic sequence information of model plants (rice and Arabidopsis), it is possible to predict the joints between adjacent exons after splicing (or termed 'intron positions' for short) in homologous ESTs of other plants. This would allow developing potential intron polymorphism (PIP) markers in these plants by designing primers in exons flanking the target intron.
We have extracted a total of 57,658 PIP markers in 59 plant species and created a web-based database platform named PIP to provide detailed information of these PIP markers and homologous relationships among PIP markers from different species. The platform also provides a function of online designing of PIP markers based on cDNA/EST sequences submitted by users. With evaluations performed in silico, we have found that the intron position prediction is highly reliable and the polymorphism level of PIP markers is high enough for practical need.
http://ibi.zju.edu.cn/pgl/pip/.
Supplementary data are available at Bioinformatics online.
随着大规模植物功能基因组测序项目的近期进展，大量的EST（表达序列标签）数据正变得可用。借助模式植物（水稻和拟南芥）的完整基因组序列信息，有可能预测其他植物同源EST中剪接后相邻外显子之间的接头（或简称为“内含子位置”）。这将使得通过在目标内含子两侧的外显子中设计引物，在这些植物中开发潜在的内含子多态性（PIP）标记成为可能。
我们在59种植物中总共提取了57658个PIP标记，并创建了一个名为PIP的基于网络的数据库平台，以提供这些PIP标记的详细信息以及来自不同物种的PIP标记之间的同源关系。该平台还提供基于用户提交的cDNA/EST序列在线设计PIP标记的功能。通过计算机模拟评估，我们发现内含子位置预测高度可靠，并且PIP标记的多态性水平足以满足实际需求。
http://ibi.zju.edu.cn/pgl/pip/。
补充数据可在《生物信息学》在线获取。
