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?
What you see on a gel or a gel image is for each pattern a set of bands, each having a certain position, you do not see base pairs or molecular weights. Therefore, BioNumerics and GelCompar II internally hold all the information about bands as relative positions, as a percentage of the length of the profile. Using a number of regression functions, the software can quite reliably transform these run lengths into base pairs or MWs, but always remember that each different regression method will give you slightly different bp or MW values. Therefore tolerances are also best entered as percentages.
If you want to enter specific tolerances in base pairs, you can transform the values as follows (example). If the largest fragment is 500bp and the smallest 50bp, then there is a range of 450bp on the gel. So 450 bp = 100%, i.e. 1 bp = 100% / 450 = 0.22%. To have an average tolerance of 1 bp in this example, you should use a setting of 0.22%.