Exonerate raw score to percent identity

Question

[tim.ivanov.92]

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?

screenshot of an output

Answer 1

[Carambakaracho]

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)

[tim.ivanov.92]

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?