I am attempting to find corresponding nucleotide sequences to a list of protein sequences that I have attained from a blastp search. So far I've attempted to find these sequences through the use of NCBI's Eutils.
I've attempted to Esearch the protein database with the given protein ID's I have, which return result object which can be further used with Elink. With Elink, I've targeted the nuccore database and gene database to find connections between protein sequence and nucleotide sequence. This has worked to some degree, but the problem I'm facing is that there seems to be no single good robust way to find a corresponding nucleotide sequence for a given protein sequence. It works for the most part, but sometimes, for example when using a protein ID that corresponds to a multispecies entry, there will be no gene link. If you instead try to elink to nuccore, you sometimes miss information in the xml output that is essential to picking out the right sequence.
Is there a robust, always working method to doing this? Every venue turns out to be more complicated than it should be.