We’re changing the company we use for pyrosequencing and they use different primer sets. I believe they’re using a primer set for fungal DNA that falls in the ITS region. Our previous pyrosequencing data covered the 16s region for fungal DNA. I’m wondering what database I should use for doing taxonomy with this data. Will the silva Eukaryote database cover fungal DNA from the ITS region. I’m in no ways an expert in this, so any guidance would be appreciated. Thanks for you aid.
The silva.eukarya.fasta covers the 18S rRNA gene sequence with no ITS data. Any way to get them to use your primers?
It isn’t likely, and the data has already been run. My boss set this up so I had no control over the parameters. Is there a database containing the ITS data that I could use to get some taxonomy data? Can I even align these if the silva database doesn’t cover ITS? Any advice would be appreciated. Thanks.
Unless your ITS sequences are from closely related organisms, they won’t align well via multiple sequence alignment. (There’s just too much variability.) The typical approach to OTU generation from ITS data is to cluster your sequences using a pairwise aligner (like the one implemented in Mothur) or CD-Hit.
Regarding taxonomy, the UNITE database covers ITS and contains well-curated, high-quality sequence data. You can download their annotated sequence files from: http://unite.ut.ee/repository.php