A member of our lab is using Primer-Blast (http://www.ncbi.nlm.nih.gov/tools/primer-blast/) to find what DNA her pairs of primers amplify in the NT nucleotide database. She designed degenerated primers and the number of possible pairs goes up to 256. She does not want to do that many primer-blasts by hand, obviously, and Primer-Blast apparently cannot use degenerate primers. I am therefore looking for a tool to automate these primer blasts.
Is there a command-line interface tool that would, given a local database of nucleotide sequences, return which sequences would amplify with a given pair of primers? It does not look like Primer-Blast can be downloaded for local and I don't think Primer3 can be used for that purpose.
My idea is to automatically generate all possible degenerate primer pairs and then run the CLI tool on them. If a program was able to directly use degenerate primers, that would be even awesomer :)
Thanks for your suggestions!