Select reference database for 18S rRNA samples sequences

Theory behind mothur
1

Hi, Because the reference database Silva.nr_v123.align is big size. i am trying pcr.seqs command. However, i don’t have oligos file, only have primer information of 18s RNA::::::
Please let me know how to reduce of Silva.nr_v123.align with primer in fasta.
Thanks for helping…

Primers::::::::
TAReuk454FWD1 (5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCAGCASCYGCGGTAATTCC-3’)and
TAReukREV3 (5’-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGACTTTCGTTCTTGATYRA-3’).

2

You need to use just the 16S rRNA gene targeted region of these primers. Those that you posted include the barcodes and adapters.

Pat