It would be great if it was possible to output the otu consensus sequence not just a representative sequence using get.oturep.
see classify.otu
Hi Pat,
Thanks for the quick response but that’s not quite what I’m looking for. I’d like to get the actual consensus sequence not consensus taxonomy. What I’m trying to do is create OTU specific probes (each OTU at the 1, 5, and 10% level). This would be great for the design of PCR and microarray probes, etc.
Currently the closest possibility is to use a program like Primrose but this is not easily automated with user supplied data. ARB probe design could also be used but it currently doesn’t allow for degenerate bases.
Thanks, Dan
Ahh… good idea. We’ll put it in the queue.
This is in version 1.15.0.
I used the consensus.seqs command yesterday and it worked quite well! I think it would be helpful, however, if the next iteration of the command included a cutoff option so users could get back a more fully resolved consensus if desired. For example, I was aligning 24 - 255bp sequences. The vast majority of ambiguities in the consensus were due to a single sequence, which I then had to go back and manually change to the correct nucleotide. If I could have set cutoff=0.97 and gotten back a sequence that only showed ambiguities for bases that were not supported by at least 97% of sequences, it would have saved me a lot of time.
Thanks for the suggestion! The consensus.seqs command will have a cutoff parameter in version 1.20.0.