I am trying to define band positions for RAPD gels and to this end, I am seeking a method which is more objective than simply lining up similarly positioned bands by eye. I have used software which quantifies approximate band size based on position and bands which are visually at the same position can often vary in size by as much as 20bp. Is there a way of assigning size boundaries, within which bands would be considered to belong to one position and not another?
There are some online program and software which may help you but these program can not count the all bands means they can only count the high intensity bands not the all...best method is with eyes..As i searched i have not found any such software which can differentiate as much as 20 bp..
you can run your fragments on the applied Biosystems (life technologies) genetic analyzer (capillary electrophoresis ) and using the gene mapper software you will be able to do what you want.
I have used several software for band matching and size measurement such gene profiler, one-D scan etc. they work good. However, in some cases you should use your eye to detect some weak bands which you recognize. Other good way to use high concentration of agarose e.g. 2% or the best use polyacrylamide 6% which will separate your bands better. All the best.
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