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PIP: a database of potential intron polymorphism markers.

Long Yang1, Gulei Jin, Xiangqian Zhao

  • 1Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, China.

Bioinformatics (Oxford, England)
|June 5, 2007
PubMed
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Researchers developed a new method to predict intron positions in plant ESTs, enabling the creation of over 57,000 potential intron polymorphism (PIP) markers across 59 species. This database facilitates marker discovery and design for plant genomics research.

Area of Science:

  • Genomics
  • Bioinformatics
  • Plant Science

Background:

  • Large-scale plant functional genome sequencing projects generate vast express sequence tag (EST) data.
  • Genomic sequences of model plants like rice and Arabidopsis enable prediction of intron positions in homologous ESTs of other plant species.
  • This prediction facilitates the development of potential intron polymorphism (PIP) markers.

Purpose of the Study:

  • To develop a method for predicting intron positions in plant ESTs.
  • To create a comprehensive database of PIP markers.
  • To provide a tool for online PIP marker design.

Main Methods:

  • Utilized complete genomic sequences of model plants to predict intron positions in homologous ESTs.
  • Developed a web-based database platform (PIP) to store and present PIP marker information.

Related Experiment Videos

  • Implemented an online tool for designing PIP markers based on user-submitted cDNA/EST sequences.

    • Main Results:

    • Successfully extracted 57,658 PIP markers across 59 plant species.
    • Established a web-based platform (PIP) detailing marker information and inter-species homology.
    • Demonstrated high reliability of in silico intron position prediction and sufficient polymorphism levels for PIP markers.

    Conclusions:

    • The developed PIP marker prediction method is reliable and effective.
    • The PIP database and online design tool offer valuable resources for plant genomics.
    • PIP markers show high polymorphism, suitable for practical applications in plant research.