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.

Gel images looking dithered

I have a problem with processing gel images in that they look fuzzy or pixelated when processing. Below is a sample of how the gels look like in the software. Previously analyzed gels in the same database look sharp, but not new ones.

Dithered gel image

Combined analysis of fingerprint data

This tutorial illustrates how to create a dendrogram based on fingerprint data coming from different experiments, using a composite data set.

Importing VNTR sequencer curve files

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

Importing peak data from peak table files

This tutorial describes how to import band size and band position tables. During import fingerprints are reconstructed based upon the size and the amplitude (area or height) of the peaks.

Clustering fingerprint data

This tutorial illustrates how to calculate a dendrogram based on banding patterns.

Demo raw spectra

A set of raw MALDI-TOF spectra from different species and isolates saved as mass-intensity lists (txt).

Importing and processing gel images

This tutorial illustrates how to import and process gel images with BioNumerics. The processing steps include lane finding, background subtraction, normalization and band definition. As sample data, a set of Pulsed Field Gel Electrophoresis (PFGE) gel images is provided, although the same principles are applicable for other typing methods using gel electrophoresis.

Band matching and polymorphism analysis

This tutorial illustrates how to create band matching tables. Band matching has a number of important applications such as screening for genetic markers (eg. using AFLP) in plant and animal breeding and microbial community analysis using PCR-DGGE, t-RFLP, ARISA or DHPLC.

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