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I want to compare two secondary structures of aligned proteins. I do not know exactly how to do it well.

Example:

EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHHHHHHHHHCHCCTHHEEEETTTEEECTTTEEECTTTEEC

EEEHHHHHHHTTTTTTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCCCCCCCEEEEEEEEEEEEEE

Example of matching:

EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHHHHHHHHHCHCCTHHEEEETTTEEECTTTEEECTTTEEC
|||        |||||| |||                    |||||||||     ||||||      |   |||    ||
EEEHHHHHHHTTTTTTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHEEEECCCCCCCCCCEEEEEEEEEE

Hypothetically: 50% aligned - > score 0.5 - > thats scoring is wrong:

EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHHHHHHHHHCHCCTHHEEEETTTEEECTTTEEECTTTEEC
||||||||||||||||||||||||||||||||||||||||||
EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHEEEEEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHH

This case will have similar score...

This is a puzzle for me, I don't know how to approach it technically.

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    $\begingroup$ Normally 3D structures of protein are compared and the RSMD is reported. How did you get your SS, with JPred or from PDBs? Comparing SS might result in some biases: if one of the two protein is getting used as a template for the other say or if both are from PDBs but the SS was called different (if so, use DSS on both). Also note that JPred is like 75% accurate at best. $\endgroup$ – Matteo Ferla Dec 15 '19 at 21:49
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    $\begingroup$ @MatteoFerla I suspect that these are predicted secondary structures. $\endgroup$ – James Dec 16 '19 at 10:02
  • $\begingroup$ @James Exactly my worry (I see a helix of a single AA in a coil). The solution is straightforward, but I am not sure how one could add error estimates to said solutions, which seems like a must... $\endgroup$ – Matteo Ferla Dec 16 '19 at 10:15
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    $\begingroup$ I suppose using data from JPred, PSIPRED, SPIDER2 and doing the 9 pairwise alignments would suffice on a push. $\endgroup$ – Matteo Ferla Dec 16 '19 at 10:20
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    $\begingroup$ @MatteoFerla I agree. In lieu of a structure, usually, a meta-prediction would suffice. I think MTG should add why the sequences are being aligned. I think different tools should be used depending on if they are checking to see how much secondary structure prediction error is in a sequence compared to a reference sequence, or if they are checking secondary structure as a proxy for structural divergence. $\endgroup$ – James Dec 16 '19 at 10:28
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Hey i solve this simply by use of SOV alghoritm. https://www.researchgate.net/publication/319526145_A_modified_definition_of_Sov_a_segment-based_measure_for_protein_secondary_structure_prediction_assessment

cheers

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