question on aligner

Commands in mothur
1

Dear Dr Schloss

I am trying to align few thousand reads using align.seqs command. I want to use silva Bacterial references (14,956 sequences) database as a template alignment.

For using the Greengenes database as template alignment, I can see the core_set_aligned.imputed.fasta when I download the Greengenes.alignment zip file. But when I download the silva Bacterial references and unzip it I do not see and core_set_aligned.imputed.fasta file. I do see some other files such as 1) nogap.bacteria.fasta 2) silva.bacteria.fasta etc.

My question is which one will be used as template alignment out of these files?

Thank you for offering such a wonderful open source program for community analysis.

Gurdeep

2

Sorry - we don’t have the core_set database (from greengenes) aligned to the silva alignment. If you want to use the silva reference alignment that I created you would use silva.bacteria.fasta. Alternatively, you could align the core_set to the silva.bacteria.fasta and then use that as the reference alignment…

align.seqs(candidate=core_set_aligned.imputed.fasta, template=silva.bacteria.fasta)

This should create core_set_aligned.imputed.align. Keep in mind that our silva reference alignment has >2-fold more sequences than the core_set.

Hope this helps…
Pat

3

Thanks for your prompt reply