Align.seqs with the pr2 database

Commands in mothur
1

Hello,

I am trying to align my sequence with the pr2 reference alignment. I have the latest download for the pr2 database compatible with mothur. Since I don’t know what the sequence start and end would be, I have an oligos file with my forward and reverse primers in this format:
forward CCAGCASCYGCGGTAATTCC
reverse ACTTTCGTTCTTGATYR

My command looks like this:
mothur > pcr.seqs(fasta=pr2_version_4.14.0_SSU_mothur.fasta, oligos=v4_forward_reverseprimer.oligos)

I rename the file:
mothur > rename.file(input=pr2_version_4.14.0_SSU_mothur.pcr.fasta, new=pr2.v4.fasta)

When I try to use align.seqs:
mothur > align.seqs(fasta=stability.trim.contigs.unique.fasta, reference=pr2.v4.fasta)

I get the error:
[ERROR]: template is not aligned, aborting.

any advice on aligning?

Thanks!

2

Hi there,

I’m sorry but I’m not familiar with the pr2 database. Based on the error message, I suspect it might not be aligned. If you open pr2_version_4_14.0_SSU_mothur.fasta could you post one of the sequences?

Pat

3

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