I have 454 based metagenomic sequencing (rRNA) reads that I was asked to blast against bacterial 16S rDNA. So far I was unable to find a data source (fasta file) that would have only these sequences for all known, sequenced organisms.
Does anyone know a good source for it? Also I would appreciate a link to a good introductory paper on the methodology. I found a bunch of papers based on 16S data but most skip the essential part of how to actually do the mapping and what problems/challenges should I be looking out for.
Thanks a lot for your help!