I have lots of ITS2 sequences and have assigned taxonomy to most using BLAST against the UNITE db. I have some sequences though that are recognized as fungi when I blast against nr but these typically show as fungi; environmental samples. I would like to try to get a rough idea of how they relate to other fungal lineages.
Thank for your answer Matt. The problem is when the blast matches are to sequences annotated as fungi; environmental sample!
Hi Paul,
I think the variable region of ITS2 is useful to discern the organism to species and even sub-species level, with the aids of secondary structure information. Of course, the alignment is always difficult when comes to the highly variable ITS2. If you have the secondary structure of the ITS2 of your fungal, the alignment can be improved by using 4SALE (http://4sale.bioapps.biozentrum.uni-wuerzburg.de/index.html), in which it align not only based on sequence but also the secondary structure information. The seq-struc alignment dataset can later be analyzed in ProfDistS (http://profdist.bioapps.biozentrum.uni-wuerzburg.de/cgi-bin/index.php) for phyologenetic inference.
I have been working on Pseudo-nitzschia species (marine diatom) and this works well for many other genus. It gives a high phylogenetic resolution even to the species complexes, cryptic and pseudocryptic species.
Hope this help.
Cheers, HongChang
Paul,
I agree with you: there is a small proportion of fungal ITS sequences that defies all attempts at taxonomic assignment even at the phylum level. That said, in nearly all (other) cases, assignment at the phylum (or better) level is possible if you know your way around in BLAST, GenBank, and UNITE.
I'm curious about your sequences. Could you send me one or two of them, such that I can have a go on my own?
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