Hi all,
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.
Thanks for your response. So it refer to ORF prediction; however the translated contig sequences is required for searching conserved domain, for example. Among several ORF prediction tool, which software do you recommend for this tasks?