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?
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tim.ivanov.92 •
From exonerate's user manual:
Alignment Scores
Currently, only the raw alignment scores are displayed. This score just is the sum of transistion scores used in the dynamic programming. For example, in the case of a Smith-Waterman alignment, this will be the sum of the substitution matrix scores and the gap penalties.
Conversion of the raw score is unnecessarily complicated, but with --ryo roll your own option you can somehow use
--ryo
%p[is]
Percent {id,similarity} over the equivalenced portions of the alignment. (ie. %pi == 100*(%ei / %et))
It's been ages since I used exonerate, last memory is me having troubles compiling the 2.4.0 binary (which might be completely wrong)
Thank you, that helps - i forgot about ryo option because i was using biopython's wrapper to parse the output. Since we are here - do you know if i am able to access ryo format options from biopython?
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