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.

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.

Clustering fingerprint data

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

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.

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.

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.

Importing and processing VNTR 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 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.

Importing and processing Agilent 2100 BioAnalyzer curve files

The 2100 BioAnalyzer is a capillary electrophoresis instrument from the company Agilent. The generated electropherograms can be exported from the Agilent 2100 BioAnalyzer software in csv format and imported in BIONUMERICS after installation of the Import fingerprint tools plugin. In this tutorial the installation of the Import fingerprint tools plugin and the import and processing of Agilent 2100 BioAnalyzer curve files is covered.

Importing and processing AATI Fragment Analyzer curve files

The Fragment Analyzer is a capillary electrophoresis instrument from the company Advanced Analytical Technologies (http://www.aati-us.com). The generated electropherograms can be exported from the AATI PROSize® data analysis software in csv or txt format and imported in BIONUMERICS after installation of the Import fingerprint tools plugin. In this tutorial the installation of the Import fingerprint tools plugin and the import and processing of the AATI Fragment Analyzer curve files is covered.

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.

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