As my title mentioned, could you please give me some suggestions about the BLASTP criteria of identifying paralogous and orthologous genes among a few species. The species I am analyzing do not have much sequencing data in NCBI, but our lab recently generate HT-seq data for them.
I found evalue of 1e-5 is not strict enough for para- or ortho- identification. I think it is necessary to further limit the criteria. I found a paper (Bioinformation. 2011; 6(1): 31) used >60% sequence identity and >80% alignment length, but I am not certain if it is a general rule.
Any of your answers will be highly appreciated! THANKS!