text: user1224: 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.
  
  user1224: 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
  
original_text: 1224: <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>
   1224: <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>
  