9.5 years ago by
This is a common issue: the development of what look like very similar resources by different groups, leading to the problem of which to use. It happens for a variety of reasons (often "historical") and there is no easy answer to your question.
One approach is to read the documentation and the associated publications for each resource, to see if the developers explain why they created it and if they compare their work to existing resources. Here are publications describing RDP, SILVA and Greengenes.
At the websites you could start with background (SILVA), objectives (Greengenes) and history (RDP).
Another approach is to search for third party comparisons. This PLoS ONE article looks useful in that regard. It briefly compares the 3 tools and seems to conclude that Greengenes provides the best combination of speed and quality.
Ultimately, your choice depends on precisely what you want to do. Do you need eukaryotic sequences? Do you need the most "comprehensive" database; i.e. the most sequences? How much error are you willing to tolerate? Sometimes it comes down to: which tool makes retrieval of the data you want easiest? Needless to say, it's important to consult with as many experts in the field as possible.
Another possibility: don't make a choice. Try to fetch the subset of data you need from all 3 sources. That way, you can do a comparative study, which can be valuable information in itself.