align.seqs

To find the start and end position of a primerset in the Silva database one should align a 16S rRNA amplicon that was amplified with these primers to the SILVA database using align.seqs.

To get the amplicon, I wrote a small R-script that saves the amplicon in a fasta file, but could not be bothered to give the sequence a proper identifier resulting in:

TACGGAGGGTG…

I used this fasta file in align.seqs as candidate and SILVA V119 as template. Unfortunately this always failed and it took me a while to realize it was because of the empty sequence identifier.

Maybe it’s not really a ‘bug’, but maybe an error message saying ‘No sequence identifier found’ could be useful?

Cheers!