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.

Data set leveled database

A set of capillary electrophoresis profiles (= electropherograms) produced by a Beckman automated sequencer (.SCF files). 

Gel image is not correctly displayed in the Processing window

I am able to import my gel image in the database, but the image is not correctly displayed in the Raw data step in the Gel processing window. What could be wrong?

Selecting a fingerprint processing window

I work with lab-on-a-chip data and for processing I prefer the classic gel processing window over the new curve processing window that appears now. How can I get the old window back?

Importing AFLP sequencer curve files

This tutorial illustrates how to import and process raw sequencer curve files as produced by the capillary electrophoresis equipment.

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.

DGGE sample data

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

Lab-on-a-chip systems

Our lab is planning to purchase a lab-on-a-chip system to replace traditional slab gel electrophoresis. I was wondering which systems are compatible with BioNumerics?

Calculating a PCA and an MDS on a fingerprint data set

This tutorial illustrates how to calculate a Principal Components Analysis (PCA) and a Multi Dimensional Scaling (MDS) (sometimes also called Principal Coordinates Analysis (PCoA)) on a fingerprint data set and how to change the layout of the obtained plots.

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