Sorry ahead of time, RNA-Seq and bioinformatics is something I am new at and still learning as I go. I am trying to compare the sequences of a single gene across different species using RNA-Seq data to identify (structural) variants or anything mutations in different species that may impact function. Thankfully there is already a reference CDS of the gene, on NCBI, that I am focusing on.
The issue I am encountering is that I do not know of the proper workflow or methodology to compare this one gene across multiple species. Ultimately I may be, and probably am, overthinking and overcomplicating the process. Is it as simple as using BLAST with the gene or my RNA-Seq data as a reference? Any advice or suggestions would be much appreciated.