I used the specific primers S-C-Act-0235-a-S-20 and S-C-Act-0878-a-A-18 in order to Identify actinomycetes. Do you think those sequence are enough to draw phylogenetic tree or I should use 8F and 1492R primers for drawing the tree?
use, 8F/1492R because the sequences deposited in RDB server used to align your seq are full length 16s sequences.
Dear Mansooreh,
It depends on your research purposes. If you are dealing with non-cultivated actinomyces, i.e. clones, you could use these primers to draw a phylogenetic tree as it will select the actinomycetes from the other bacterial DNA.
However, the obtained fragment will be only 642 bp long and sometimes it is not suffice to obtain a high resolution phylogenetic tree.
On the other hand, if you are working with isolates, I recommend you to use the other set of primers which will give sequences of ~1400 bp long and therefore a more robust phylogenetic analysis.
Also, you could use the EzTaxon e-server (http://www.ezbiocloud.net/eztaxon) to analyse your sequences.
Good luck with your research!
Zucchi
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