I would like to download all the possible 16S rDNA sequences of bacterial species only. I tried Ribosomal Database Project (RDP) but I think it could be done only manually. I would like to donwload at once. So, is there any way to download all together at once?
You can download the rRNA sequences from Rfam (family RF00177). Go to the Alignments tab (here: http://rfam.sanger.ac.uk/family/RF00177#tabview=tab2 ) and under Formatting options select Full, FASTA (ungapped) format and download and there you go. You should only change the U's to T's to get the DNA.