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.?
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.
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.?
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?
How do I delete a reference system?
How do I combine my two fingerprint types into one dendrogram?
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?
What is the difference between the Jaccard and Dice coefficient for band matching?
Is it possible to define target regions on my gels to be used for comparison, for example between 100 and 500 bp?
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?
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?
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?