Phytoplasma pp 329-338 | Cite as

The iPhyClassifier, an Interactive Online Tool for Phytoplasma Classification and Taxonomic Assignment

  • Yan Zhao
  • Wei Wei
  • Ing-Ming Lee
  • Jonathan Shao
  • Xiaobing Suo
  • Robert E. Davis
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 938)

Abstract

The iPhyClassifier is an internet-based research tool for quick identification and classification of diverse phytoplasmas. The iPhyClassifier simulates laboratory restriction enzyme digestions and subsequent gel electrophoresis and generates virtual restriction fragment length polymorphism (RFLP) patterns. Based on RFLP pattern similarity coefficient scores, the iPhyClassifier gives instant suggestions on group and subgroup classification status of the phytoplasma strains under study. The iPhyClassifier also aligns the query sequences with that of reference strains of all previously described ‘Candidatus Phytoplasma’ species, ­calculates sequence similarity scores, and assigns the phytoplasmas under study into respective ‘Ca. Phytoplasma’ species as related strains according to the guidelines set forth by the Phytoplasma Taxonomy Group of the International Research Program on Comparative Mycoplasmology. Additional functions of the iPhyClassifier include delineation of potentially new phytoplasma groups and subgroups as well as new ‘Ca. Phytoplasma’ species. This chapter describes the program components, the operational procedure, and the underlying principles of the iPhyClassifier operation. The chapter also provides hints on how to interpret the results.

Key words

Candidatus Phytoplasma’ species assignment iPhyClassifier Phytoplasma classification Restriction fragment length polymorphism Similarity coefficient 

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Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Yan Zhao
    • 1
  • Wei Wei
    • 2
  • Ing-Ming Lee
    • 3
  • Jonathan Shao
    • 1
  • Xiaobing Suo
    • 1
  • Robert E. Davis
    • 4
  1. 1.Molecular Plant Pathology LaboratoryUSDA-Agricultural Research ServiceBeltsvilleUSA
  2. 2.Institute for Bioscience and Biotechnology ResearchUniversity of MarylandCollege ParkUSA
  3. 3.Molecular Plant Pathology LaboratoryUSDA, ARSBeltsvilleUSA
  4. 4.USDABeltsvilleUSA

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