Question: Exonerate raw score to percent identity
0
gravatar for tim.ivanov.92
12 months ago by
tim.ivanov.9210 wrote:

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

ADD COMMENTlink modified 12 months ago by Carambakaracho2.2k • written 12 months ago by tim.ivanov.9210
2
gravatar for Carambakaracho
12 months ago by
Carambakaracho2.2k
Germany/Cologne
Carambakaracho2.2k wrote:

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)

ADD COMMENTlink modified 12 months ago • written 12 months ago by Carambakaracho2.2k

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?

ADD REPLYlink written 12 months ago by tim.ivanov.9210
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1542 users visited in the last hour