title: The iPhyClassifier, an interactive online tool for phytoplasma classification and taxonomic assignment.
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.
authors.affiliation: Molecular Plant Pathology Laboratory, USDA-Agricultural Research Service, Beltsville, MD, USA. yan.zhao@ars.usda.gov
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhao
authors.forename: Wei
authors.initials: W
authors.lastname: Wei
authors.forename: Ing-Ming
authors.initials: IM
authors.lastname: Lee
authors.forename: Jonathan
authors.initials: J
authors.lastname: Shao
authors.forename: Xiaobing
authors.initials: X
authors.lastname: Suo
authors.forename: Robert E
authors.initials: RE
authors.lastname: Davis
mesh_terms: D019295:Computational Biology / Q000379:methods*; D020407:Internet; D045582:Phytoplasma / Q000145:classification* / Q000235:genetics; D012150:Polymorphism, Restriction Fragment Length; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012984:Software
chemical_list: D012336:RNA, Ribosomal, 16S