I have a species with an unannotated reference FASTA. I have gene coordinates that I pulled from NCBI from very closely related annotated species (each gene is 10,000 - 30,000BP long.) I want to map these genes to the unannoated reference FASTA so that I can have have coordinates for this new species. I've been using a combination of BLAST and BLAT, but it's been hard to figure out exactly the start and end of this gene, in the unannotaed species.
Any help would be appreciated!