I use augustus gene prediction software since my organism is a unicellular eukaryote.From my nucleotide dataset I am more concentrating on membrane proteins.
I trained augustus with input of "genome file" and Protein file for "training". The protein file contained some incomplete transmembrane protein sequences. After training, I used this information to predict genes. I found a single gene being predicted as several genes. Usually this was common for Transmembrane proteins.
I dont have very nearby relative whose transmembrane protein sequences are available with annotation. Any suggestions to overcome this problem?