Importing VNTR sequencer curve files

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

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.

Download sample data: 
VNTR sequencer trace files
Multi-Locus VNTR (MLVA) data ran on an Applied Biosystems 3730 DNA Analyzer, raw data (.fsa files). Eight VNTR targets per sample were amplified: two pools were generated, each containing four PCR products, using four fluorescent dyes (6-FAM, VIC, NED, and PET).
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