I have done a de novo transcriptome assembly for a non-model plant. I have then tried to predict ORFs using Transdecoder tool. Finally, I removed asterisk characters in the "file1.transdecoder.pep" by the command of "sed -i 's/*//g' file.fasta" and did blastp against some databases. But, I found that there is much differences between the blastp and blastx (that I also conducted it for the same databases) outputs. In fact, the maximum of ortholog hit ratio (OHR) for blastx was 1 while it was 0.5 for blastp. As you know, the OHR near to 1 represent the full-transcript and highly desirable. Could you please share your opinion about it and let me know which is wrong for blastp?
Thanks so much for you help.