Band search settings
What does "Minimum profiling" and "Minimum area" for band searching mean? How can I relate the setting for these values to other metrics such as 'rfu'.
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.
What does "Minimum profiling" and "Minimum area" for band searching mean? How can I relate the setting for these values to other metrics such as 'rfu'.
My gels each have two or more identical reference lanes which I use to align with the active reference system. Do I need to create a new database entry for each reference lane?
I have loaded patterns obtained with two different restriction enzymes onto the same gel. Can I tell the software that these patterns belong to two different fingerprint types?
When I perform auto-assign bands to normalize my gels, the software doesn't always assign the right bands. I need to do a lot of manual assigning work. Is there a way to optimize this?
How can I define a standard lane for my reference system? What is the function of a standard lane?
How do I get/choose the active reference system for new gels?
How can I obtain a list of fragment sizes or molecular weights of the bands per lane or per selection?
How can I obtain band sizes (fragment lengths) for my gels?
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?
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?