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phytoplasma resource center

Virtual Gel Analysis

Virtual RFLP analysis of DNA sequences


Automated Calculation of Similarity Coefficients

virtual gel               click here to view virtual gel RFLP patterns

iPhyclassifier and virtual gel analysis, best veiwed using the firefox browser

Updated August 11, 2009

This is an example of virtual RFLP patterns of a 16S rDNA nucleotide sequence that was “digested”in silico with 17 restriction endonuclease enzymes. The nucleotide sequence of this 16S rDNA (from cactus witches’-broom phytoplasma) was obtained from the GenBank database (GenBank accession number EU099547). This phytoplasma was originally classified, in 16S rDNA RFLP group 16SrII, on the basis of RFLP patterns that were obtained after actual, wet lab enzymatic digestion of 16S rDNA amplified in the polymerase chain reaction (PCR); classification based on the virtual gel patterns shown here is in complete agreement with the original, wet lab-based classification.

Wei Wei, Robert E. Davis, Ing-Ming Lee and Yan Zhao. Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups. International Journal of Systematic and Evolutionary Microbiology (2007), 57, 18551867 link


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