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.

Internal reference positions

I am having trouble with the normalization of internal reference positions. After selecting Normalization > Update Normalization, the bands do not move and the arrows remain. Why do the internal reference positions not normalize?

Weight setting for fingerprints

Where does the "weight" number come from in the pairwise comparison window?

Linking a standard to a new reference system

Is it possible to link a new standard with a new reference system in the same fingerprint type? The software doesn't want to assign the standard except with the first reference system I have entered.

Band quantification values

When a band matching table is created from a composite data set originated from one or more fingerprint type experiments, what is the interpretation of the numerical values?

Bootstrap analysis on gel data

How can I perform a bootstrap analysis on gel data?

Gel card

When I click on the button in the entry card, to pop up the gel strip, nothing but a very small window appears, on which I cannot even see the gel strip.

Showing polymorphic bands only

Is it possible to identify subsets of bands which are common to groups of isolates, which may then be used in turn as bands for identification of species, serogroups etc.?

Display profiles as reconstructed images

In the old GelCompar software, I could choose to display the patterns as reconstructed images rather than TIFF gel strips. How can I do this in BioNumerics or GelCompar II?

Combining fingerprint profiles

How do I combine my two fingerprint types into one dendrogram?


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