Importing and processing a DGGE gel image

Denaturing Gradient Gel Electrophoresis of amplified 16S rDNA (commonly denoted as DGGE or PCR-DGGE) is a technique frequently used for bacterial community fingerprinting in microbial ecology. This tutorial illustrates how to import a DGGE gel image into your BioNumerics database, how to process the image, and how to calculate diversity indices on the imported DGGE profiles.

Fingerprints

Any type of data that can be translated into a densitometric curve is considered a fingerprint type in the BioNumerics and GelCompar II software. This includes commonly used genotyping methods employing agarose or polyacrylamide slab gel electrophoresis (PFGE, rep-PCR, RAPD, PCR-DGGE, etc.), in which case the data are usually imported as two-dimensional gel images (bitmaps). Another major group consists of capillary electrophoresis profiles such as AFLP, ARISA, T-RFLP, etc. Here, the raw electropherograms generated by an automated sequencer (genetic analyzer) or derived peak table text files can be imported. Finally, any other profile (generated e.g. by gas chromatography, HPLC or spectrophotometry) that can be seen as peaks or bands, can be analyzed as a fingerprint.

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DGGE sample data
Gel images containing DGGE profiles of bacterial 16S rDNA gene fragments that were amplified using proteobacteria specific primers.
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