Does anyone know what exactly does line “raw score” in exonerate output mean?
For example I attach here a screenshot of a full hit, where the length of a query is 74bp, yet the raw score is 370, which is much greater than 74. The original command was:
exonerate --verbose 0 -E --model affine:bestfit --percent 20 --singlepass 1 --showtargetgff 1 query.fasta target.fasta > exonerate_out.out
Can you explain what exactly raw score means, and how do I transform it to percent identity?