Most of the publications mention 28F, but some papers mention 27F, so which one is best? For the environmental samples. My target is bacterial community findings.
a good test is to confront your diffrent "potential" primer pairs to a database in order to check for their universality. You can try the Ribosomal Database Project (http://rdp.cme.msu.edu/probematch/search.jsp) and the probematch tool.
This will give you an idea of what you can theoretically amplify. Also, regarding 454 technique, you need to keep in mind that you will get about 500 bases long fragments (800 with the new kits). Usually, the most resolutive 16S fragment comprise variable regions V3, V4, V5. You can also take a look at the HMP protocols, they chose different primer set that are actually pretty good.
If you want to go further in the analysis of 16S domains, I can suggest you this very interesting paper --> http://www.ncbi.nlm.nih.gov/pubmed/14607398
Good luck for your work
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