Possible miscalculation

[michalfilippi]

Hi,
I was implementing SOV score calculator as well and I tried to compare my results with yours (as a sort of back check) and I found out they differ. So I dug deeper and I think there might be some error in your calculation.

For example, according to original article¹ about SOV score, for observation RREEERRRRRREEEEEERRR and prediction RRRRRRREEEEERRREERRR the calculated SOV score should be equal 39.4. But your program returns 42.56.

I haven't tried to look for the exact code section causing this.

Have a good day and thank you for publishing your code. :) It helped me.

Michal

[1] : A Zemla, C Venclovas, K Fidelis, and B Rost. A modified definition of sov, a segment-based measure for protein secondary structure prediction assessment. Proteins, 34(2):220–3, 1999.

[mircare]

Hi,

I have just noticed that your SOV score sometimes differs from http://proteinmodel.org/AS2TS/SOV/sov.html -- e.g., http://as2ts.proteinmodel.org/AS2TS/DATA/JOBS/job_85611_180831_13r/SOV_85611.html -- and http://dna.cs.miami.edu/SOV/.

Best,
Mirko

[nanjiangshu]

Hi Mirko, Thanks for pointing that out. Could you please send me an example so that I can debug? Best, Nanjiang

…

On 31 Aug 2018, at 11:30, mircare ***@***.***> wrote: Hi, I have just noticed that your SOV score sometimes differs from http://proteinmodel.org/AS2TS/SOV/sov.html <http://proteinmodel.org/AS2TS/SOV/sov.html> -- e.g., http://as2ts.proteinmodel.org/AS2TS/DATA/JOBS/job_85611_180831_13r/SOV_85611.html <http://as2ts.proteinmodel.org/AS2TS/DATA/JOBS/job_85611_180831_13r/SOV_85611.html> -- and http://dna.cs.miami.edu/SOV/ <http://dna.cs.miami.edu/SOV/>. Best, Mirko — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFkD-kL6s02z2y9_XhNXghCeJt5jMvFYks5uWQImgaJpZM4NFW18>.

[nanjiangshu]

Sorry. You did give me the example already. Best, Nanjiang

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On 31 Aug 2018, at 12:03, Nanjiang Shu ***@***.***> wrote: Hi Mirko, Thanks for pointing that out. Could you please send me an example so that I can debug? Best, Nanjiang > On 31 Aug 2018, at 11:30, mircare ***@***.*** ***@***.***>> wrote: > > Hi, > > I have just noticed that your SOV score sometimes differs from http://proteinmodel.org/AS2TS/SOV/sov.html <http://proteinmodel.org/AS2TS/SOV/sov.html> -- e.g., http://as2ts.proteinmodel.org/AS2TS/DATA/JOBS/job_85611_180831_13r/SOV_85611.html <http://as2ts.proteinmodel.org/AS2TS/DATA/JOBS/job_85611_180831_13r/SOV_85611.html> -- and http://dna.cs.miami.edu/SOV/ <http://dna.cs.miami.edu/SOV/>. > > Best, > Mirko > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub <#1 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFkD-kL6s02z2y9_XhNXghCeJt5jMvFYks5uWQImgaJpZM4NFW18>. >

[nanjiangshu]

Hi @mircare. I've rewrote the function for CalSOV() and now it returns the same result as in http://proteinmodel.org/AS2TS/SOV/sov.cgi. It is fun to write the code in c++ again although I have moved to the Python world many years ago :)

Best,

Nanjiang