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ITS reference alignment

Posted: Thu May 10, 2018 8:12 am
by peleliu
Hi,
Is there a good reference alignment for usage with ITS data in align.seqs?
I tried ITSdb.findley.fasta but got an error that the template is not aligned and Mothur aborted.
Any suggestions?
Thanks!

Re: ITS reference alignment

Posted: Wed May 16, 2018 4:41 am
by kmitchell
In general, ITS evolves too quickly to be aligned. If you are working with just a small taxonomic group, you could create you own alignment. But if you are working with all fungi, you can not align ITS/ITS2

Re: ITS reference alignment

Posted: Wed May 16, 2018 8:32 am
by peleliu
OK then, what are the preferred primers (the "16S equivalent") for working with fungi?

Re: ITS reference alignment

Posted: Fri May 25, 2018 1:12 pm
by kmitchell
sorry, missed your followup. I do use ITS2 even though we can't align it. It gives the best taxonomic resolution that we can get for all fungi. If you are working with specific groups of fungi, you may want to choose a different target.