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Bioinformatics Advance Access originally published online on June 1, 2007
Bioinformatics 2007 23(16):2174-2177; doi:10.1093/bioinformatics/btm296
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PIP: a database of potential intron polymorphism markers

Long Yang , Gulei Jin , Xiangqian Zhao , Yan Zheng , Zhaohua Xu and Weiren Wu *

Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, China

*To whom correspondence should be addressed.


  Abstract

Motivation: 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.

Results: 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.

Availability: http://ibi.zju.edu.cn/pgl/pip/

Contact: wuwr{at}zju.edu.cn

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alfanso Valencia

Received on March 18, 2007; revised on May 12, 2007; accepted on May 25, 2007

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