Get.seqs for BLAST?


I have an Ion Torrent run that I have classified with both the SILVA and GG databases. I am particularly interested in the cyanobacteria sequences which in both databases largely return unknowns for my data. I am trying to figure out how to remove those sequences from my summary taxonomy file to create a fasta to BLAST. Does anyone know a way to do this? I think if I create an accnos file from the taxonomy file of my cyano sequences and run get.seqs with my group file I can remove just those sequences then convert to a fasta. Anyone know if I’m on the right track or of another way to do this?

Thanks for any help :smiley:

Get.lineage is what you’ll want. For your Greengenes classiication it should be as simple as:

get.lineage(fasta=bjconroy87.fasta, count=bjconroy87.count_table,, taxon=p__Cyanobacteria)

It will be very similar for the SILVA taxonomy, just without the ‘p__’ tag.