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.

Defining a standard lane

How can I define a standard lane for my reference system? What is the function of a standard lane?

Set active reference system

How do I get/choose the active reference system for new gels?

Obtaining a list of fragment sizes

How can I obtain a list of fragment sizes or molecular weights of the bands per lane or per selection?

Obtaining fragment lengths

How can I obtain band sizes (fragment lengths) for my gels?

Changing fingerprint type settings

I already have a number of gels stored in my database, and wish to improve the settings for the fingerprint type. Which settings can I safely change and which not?

Use the current settings as new defaults

Sometimes, when I save and close a gel window, the program asks me "Settings have been changed. Do you want to use the current settings as new defaults?" What does this mean?

Configuration has been changed

Sometimes, when I close a gel processing window, the program asks me "Configuration has been changed. Do you want to save the changes?" What does this apply to?

Rescale curves

In the normalization part of the software, the curves in the right panel are very flat, with peaks almost invisible. Can I change this?

Delineating gel images

How important is the delineation of a gel by the green rectangle?

Compatible capillary sequencers

What automated sequencers is BioNumerics or GelCompar II compatible with?


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