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
- is it ok to align the 18S V9 sequences using the whole silva.nr_v138_1.align database as reference ?
- 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)