I am trying to find protein/nucleotide sequence homolog of one species (A.0) in a related species (A.1). The gene in A.0 has been well annotated and deposited in ncbi. Genes in A.1 seem to be very poorly annotated and I can not find them using ncbi blast. I have performed tblastn locally but can not identify the gene when I load a mapped file in IGV because there is no gff file to tell where the gene starts and end in IGV. Is there a way you all can suggest I handle this problem without having to create annotation for the entire A.1?
Also, I plan to find transcript expression levels in transcriptom of A.1. Would it be appropriate to directly use the genes from A.0 to do this? I do not think so but what do you think?