I'd like to find all possible hits for a certain NCBI conserved domain (which is expressed as a PSSM) in a chromosome or scaffold of a certain genome. I know that the common way to search for conserved domain hits in a nucleotide sequence is to translate it into 6 ORFs and RPS-BLAST each one of them against the Conserved Domains Database (CDD). But this is reasonable for short nucleotide query sequences and not a chromosome length.
I'm thinking it might have already been done by NCBI, in which case my question would be if anyone knows which files have that info. But if I have to do that, I'm guessing some variation of a TBLASTN (where the query is the PSSM) will do. In that case any suggestion how to achieve that?