I am a new user of exonerate. I tried to map protein-evidences to whole genome assembly by using exonerate with protein2genome model. After protein-evidences mapping, I wanted to filter all obtained transcripts (exonerate output file) that have poor alignment scrores. In Liang et al article (Liang C, Mao L, Ware D, et al. Evidence-based gene predictions in plant genomes[J]. Genome research, 2009, 19(10): 1912-1923.), they generally use a sequence identity threshold of 90% for same-species alignment and of 30% (protein sequence similarity) for cross-species alignments, while I only found raw alignment score (such as 805) in output file of exonerate.
So I don't know how to filter my transcripts based on exonerate results. In other words, I can't find any sequence identity value (i.e 90%) in exonerate results. So I doubt that if there were some ways to transfer raw alignment score (i.e. 805) to sequence identity value (i.e. 90%).