What Fungal ITS database are people using?

Theory behind mothur
1

I’ve been searching for a db to use for my ITS2 pyrotags. So far I’ve found ITS2db (http://its2.bioapps.biozentrum.uni-wuerzburg.de/) and UNITE (http://unite.ut.ee/) but neither are aligned-I get the impression that the unite curators don’t think you can create a meaningful universal fungal ITS alignment. Is this other’s findings too or have you guys found a great db that I’ve missed so far?

my plan for my fungal tags:
clean following the Schloss SOP
pairwise alignment
choose several otu cutoff levels for otu matrix for stats (3,5, 8% maybe)
also create a taxonomic species matrix (id’d by blasting against ITS2db and/or Unite) and run similar community stats on that

I’m definitely in the OTU camp for Bacterial communities but just am not sure for these fungal ITS. Would love to hear how you all are working with them.

2

A year ago, UNITE was the best I could find. This ref may help for an overview of UNITE http://www.ncbi.nlm.nih.gov/pubmed?term=21949797

If I recall correctly, I had some parsing issues with their taxonomic descriptions and therefore mapped the GI’s or extracted the genus:species to NCBI taxonomy. You may also want to give their unite plutof workbench a try for comparison purposes.

Hope that will help,

Chuck