PIP: a database of potential intron polymorphism markers.
BACKGROUND
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.


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


BACKGROUND
Supplementary data are available at Bioinformatics online.
Yang
Long
L
Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, China.
Jin
Gulei
G
Zhao
Xiangqian
X
Zheng
Yan
Y
Xu
Zhaohua
Z
Wu
Weiren
W
D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D018744:DNA, Plant / Q000235:genetics*; D030541:Databases, Genetic; D019143:Evolution, Molecular; D005819:Genetic Markers / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D016247:Information Storage and Retrieval / Q000379:methods; D007438:Introns / Q000235:genetics*; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*
D018744:DNA, Plant; D005819:Genetic Markers