I want to analyze my gels with Bionumerics and I tried the same things as they explained in the videos and in the quick guide, but it does not work. When I try to create a new comparison, I do not see my bands and lanes and therefore I cannot make any comparisons. The only difference between their example gels and my gels is that I don't have a lane for marker, I did not use any marker, I only want to create dendrograms based on the bands I have in each lane. Can anyone help me with this problem?
You can use Gelcompate II, and get band info and used following artilce to interprint data:
How to get more out of molecular fingerprints: practical tools for microbial ecology ((doi:10.1111/j.1462-2920.2008.01572.x)
Did you already get the lines and bands for a single gel, and then you trying to compare with other gel?
Or you are having troubles getting lines and bands within a gel?
It is always recommended to charge internal reference lines at each side of the gel, even if there are not markers.
According to my notes:
1- Get gel file
2- Find lines - to do this go to edit then edit settings.
3- Strips - adjust thickness, spot removal and background subtraction.
4-Curves - adjust average thickness, number of nodes, background subtraction, filtering, R-L.
5- Normalization - Define reference lines, assign reference positions and normalice.
6-Auto found bands with a good profiling. Add bands if necessary (enter), or delete bands (Supr).
7-Save file - export or print report.
Yes, I got the lanes and the bands from the gel, but I don't want to compare it with another gel, I want to compare the lanes between them, because I did a fingerprinting of some communities of bacteria, on the same gel, and based on the bands you can compare each community (a lane) with the others to see how similar they are and how they will group based either on Jaccard similarity coefficient or other in order to create a dendrogram. And before I used another software like TotalLab where you can do this, but I couldn't analyze the data as I wanted, so I want to try with Bionumerics and I don't know how I can do that. And I found this from bionumerics: http://www.applied-maths.com/sites/default/files/whitepapers/Import_DGGE_gel.pdf But the software doesn't show my lanes and my bands when I want to make a comparison.
Ok,
So the problem is the absence of markers, it is the way that this particular software works.
My advise is that you export the report and use DendroUPGMA to get the dendrogram.
http://genomes.urv.es/UPGMA/
Hi Manualla,
You can always contact the Applied Maths support ([email protected]) if you have questions about the BioNumerics software. We usually get back to you within 24 hours.
Dolf Michielsen (developer @ Applied Maths)
Hi,
I have the same problem. I try to use Gelcompare but I can obtein the dendogram, maye becuse I dont have a marker. Did you find a solution?
Ana
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