Question: How to Create comparison venn diagram using SILVA,GREENGENES,RDP,NCBI and OTT databases
gravatar for jinals
22 months ago by
jinals0 wrote:

I want to compare different 16s rRNA databases like SILVA,GREEN GENES, RDP, NCBI and OTT. Now I want to compare all these databases and want to know how many same genus or species available among all these databases. What is the process or tool available to identify such similarity.

ADD COMMENTlink modified 22 months ago • written 22 months ago by jinals0

You forgot to add a question. Adding more information to the question would also be appreciated.

Also, if you show us what you tried people will be more eager to point out your mistake and put you back on the right track. We don't really like an open question like this.

ADD REPLYlink written 22 months ago by WouterDeCoster39k

Thanks for your suggestions. I added more information.

ADD REPLYlink written 22 months ago by jinals0

Venn diagrams are for depicting the sizes of intersections of sets, so you need to define what the intersection between the databases you have means and implement that first, to determine what you are going to depict. e.g. what does intersect(SILVA, NCBI) mean? Most likely this will involve some serious identifier mapping, as for obvious reasons SILVA is not a simple set but a data-base and the others as well. The only level of elements I could think this is feasible easily is the set of represented species.

ADD REPLYlink modified 22 months ago • written 22 months ago by Michael Dondrup46k
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