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.
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.
This tutorial illustrates how to import and process raw sequencer curve files as produced by the capillary electrophoresis equipment.
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.
This tutorial illustrates how to calculate a dendrogram based on banding patterns.
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.
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.