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.

Area sensitive setting

When I cluster gel patterns using a band-based coefficient, what value is used when I select "Area sensitive"? What is the function of the 'Comparative Quantification' settings in the Fingerprint type window?

Difference between Jaccard and Dice coefficient

What is the difference between the Jaccard and Dice coefficient for band matching?

Active zones

Is it possible to define target regions on my gels to be used for comparison, for example between 100 and 500 bp?

Tolerance setting for matching bands

In other gel analysis software, a maximum tolerance for matching bands is defined in molecular weight, for example +/- 2 base pairs. In BioNumerics (GelCompar II) the tolerance is in percentage. How do I relate this to bp or MW?

Band quantification settings

When I perform a band matching (composite data set) and compare the band surfaces with those listed in the gel processing window, I obtain different values for the same bands. How is this possible?

Band search settings relative to max value

When I perform an automatic band search, in some lanes too many bands are found, while in other lanes of the same gel almost no band is found. Is there a way to specify the parameters per lane?

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'.

Adding reference lanes to the database

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?

Change fingerprint type of 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?

Auto-assigning bands

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?


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