I'm currently trying to design a set of degenerate primers to amplify an identified conserved region among our target proteins, but I can't find any tool that accepts non-ATCGN degenerate nucleotides. The tools I've found either convert them to N or exclude them entirely from primer candidates. Is there any tool that can design these primers, preferably one that can perform Primer-BLAST-type functionality in checking specificity versus specific organisms?
I have used DNASTAR (https://www.dnastar.com/) to design degenerate primers for period-gene in sarcophagid flies. It worked out pretty good. I don't know if DNASTAR handles the issues you mentioned, but I thought it might be helpful to try.
I've just read a very interesting paper about it presenting an open-source software that might help. Take a look at this DOI: 10.1186/1471-2105-9-55. I haven't used it yet but if I were you I would give it a try.
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