I understand that coordinates corresponding to 27f and 1492r priming sites are used in the generation of silva.nr_v123.align
from the silva.full_v123.fasta file ( http://blog.mothur.org/2015/12/03/SILVA-v123-reference-files/ ).
27f and 1492r priming sites would turn in the full length 16S gene.
When I do a grep for fungal sequences from silva.nr_v123.align, I do see a lot of Eukaryote / Fungal sequences in there.
grep “>” silva.nr_v123.align | grep “Eukaryota” | grep -c “Fungi”
(1) So, does it imply presence of 16S molecule in eukaryotes / fungi as well ? --> Based on the above observation (i.e., grep outcomes)
(2) I understand that there are no ITS1/ITS2 portions in silva.nr_v123.align – based on the tests I did using
ITS1/ITS2 from S. cerevisea Chr12. Am I correct on this point ? Please tell me.
Please clarify. Thank you.