NCBI exposes (e.g., via eutils) genomic coordinates for current transcripts on the current assembly only. I would like coordinates for older transcript versions on newer assemblies and for newer transcripts on older assemblies, and be reasonably confident that I'm mimicking NCBI behavior as closely as possible.
Has anyone out there reproduced NCBI's invocation of splign? If so, how?
To be clear, I have splign and friends running. I'm really asking about the command line invocation and data prep.