Align.seq with silva database and classify.seq using PR2 database


I am processing my Illumina sequences (18S sequences, V9 hypervariable region) using mothur.

I have first aligned my seqences using the align.seqs() command with silva.nr_v138_1.align database (the whole database, not a customized database for 18S V9 only).

After downstream improvement of sequence quality, I classify these improved sequences using the classify.seqs() command with the PR2 database

My question is

  1. is it ok to align the 18S V9 sequences using the whole silva.nr_v138_1.align database as reference ?
  2. is it ok to align.seq using silva.nr_v138_1.align database and classify.seqs() using a different database? (as I used the PR2 database for classify.seq)

Thank you!

My only concern would be that the databases may not have the V9 region for all of your sequences. I would suggest trimming the reference for the V9 region so that you’re sure you’re only looking at references that include your region.