Answers.Body: <p>Hey i solve this simply by use of SOV alghoritm. <a href="https://www.researchgate.net/publication/319526145_A_modified_definition_of_Sov_a_segment-based_measure_for_protein_secondary_structure_prediction_assessment" rel="nofollow noreferrer">https://www.researchgate.net/publication/319526145_A_modified_definition_of_Sov_a_segment-based_measure_for_protein_secondary_structure_prediction_assessment</a></p>
  
  <p>cheers</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-01T15:48:18.407Z
Answers.LastActivityDate: 2020-04-01T15:48:18.407Z
Answers.UserDisplayName: MTG
Body: <p>I want to compare two secondary structures of aligned proteins. I do not know exactly how to do it well.</p>
  
  <p>Example:</p>
  
  <pre><code>EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHHHHHHHHHCHCCTHHEEEETTTEEECTTTEEECTTTEEC
  
  EEEHHHHHHHTTTTTTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCCCCCCCEEEEEEEEEEEEEE
  </code></pre>
  
  <p>Example of matching:</p>
  
  <pre><code>EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHHHHHHHHHCHCCTHHEEEETTTEEECTTTEEECTTTEEC
  |||        |||||| |||                    |||||||||     ||||||      |   |||    ||
  EEEHHHHHHHTTTTTTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHEEEECCCCCCCCCCEEEEEEEEEE
  </code></pre>
  
  <p>Hypothetically: 50% aligned - > score 0.5 - >  thats scoring is wrong:</p>
  
  <pre><code>EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHHHHHHHHHCHCCTHHEEEETTTEEECTTTEEECTTTEEC
  ||||||||||||||||||||||||||||||||||||||||||
  EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHEEEEEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHH
  </code></pre>
  
  <p>This case will have similar score... </p>
  
  <p>This is a puzzle for me, I don't know how to approach it technically.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-12-15T21:49:30.900Z
Comments.Text: 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.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-12-16T10:02:56.217Z
Comments.Text: @MatteoFerla I suspect that these are predicted secondary structures.
Comments.UserDisplayName: James
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-12-16T10:15:51.810Z
Comments.Text: @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...
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-12-16T10:20:34.043Z
Comments.Text: I suppose using data from JPred, PSIPRED, SPIDER2 and doing the 9 pairwise alignments would suffice on a push.
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-12-16T10:28:18.520Z
Comments.Text: @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.
Comments.UserDisplayName: James
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-12-16T17:38:39.417Z
Comments.Text: It is a predicted SS with GOR method. I try to add sorting by SS to my algorihtm. First version will use garnier (emboss) method. Sequences are aligned because program align similar sequences. Then I add SS to check aligned proteins (additional validation). I plan to use spider or jpred in future.
Comments.UserDisplayName: MTG
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-12-17T00:34:58.127Z
Comments.Text: In summary, this is a very provisional analysis, providing a starting point to further de novo prediction methods. We all assume the crystal structures are not present here
Comments.UserDisplayName: M__
Tags: <proteins><python><r><secondary-structure>
Title: protein secondary structure matching/comparison scoring
ThreadText: # protein secondary structure matching/comparison scoring
  
  (Asked by: username_0 on 2019-12-15)
  
  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.
  
  **Tags:** proteins, python, r, secondary-structure
  
  > **Comments:**
  > **username_1**: 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.  
  > **username_2**: @username_1 I suspect that these are predicted secondary structures.  
  > **username_1**: @username_2 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...  
  > **username_1**: I suppose using data from JPred, PSIPRED, SPIDER2 and doing the 9 pairwise alignments would suffice on a push.  
  > **username_2**: @username_1 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.  
  > **username_0**: It is a predicted SS with GOR method. I try to add sorting by SS to my algorihtm. First version will use garnier (emboss) method. Sequences are aligned because program align similar sequences. Then I add SS to check aligned proteins (additional validation). I plan to use spider or jpred in future.  
  > **username_3**: In summary, this is a very provisional analysis, providing a starting point to further de novo prediction methods. We all assume the crystal structures are not present here  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2020-04-01. Score: 1 | Accepted answer
  
  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
  
  
  ---
  
  