These could be useful in making a primer set. Do you know of any tools that can do in silico PCR with an extended IUPAC DNA alphabet (https://www.bioinformatics.org/sms/iupac.html)? I tried isPcr but it can't handle IUPAC characters.
How to find full length ribosomal sequences for fungi?
1 answer
There are separate blast databases for these at NCBI:
https://ftp.ncbi.nih.gov/blast/db/18S_fungal_sequences.tar.gz
https://ftp.ncbi.nih.gov/blast/db/28S_fungal_sequences.tar.gz
https://ftp.ncbi.nih.gov/blast/db/LSU_eukaryote_rRNA.tar.gz
https://ftp.ncbi.nih.gov/blast/db/ITS_RefSeq_Fungi.tar.gz
https://ftp.ncbi.nih.gov/blast/db/SSU_eukaryote_rRNA.tar.gz
You can dump out the sequences if needed from these.
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There are several million species of fungi. Did you have one in mind?