How to find full length ribosomal sequences for fungi?

Question

[O.rka]

I'm either looking for a tool that can extract full length ribosomal sequences including SSU/LSU and ITS regions OR a database of these sequences. I was thinking it might be in NCBI's nt but that might just be for either SSU, LSU, or ITS and not together.

[seidel]

There are several million species of fungi. Did you have one in mind?

Answer 1

[GenoMax]

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.

[O.rka]

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.