Body: <p>I am confused about the difference between sequence-independent and sequence-order independent structural alignment. TM-align for example claims to be sequence-independent; however, I've seen it is also sequence order independent from the papers. To me, they sound like the same thing, but obviously, they aren't. Does anyone know about anything the difference?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-08-30T12:04:50.923Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-08-16T16:52:05.080Z
Comments.Text: TM-align is an algorithm for sequence independent protein structure comparisons. For two protein structures of unknown equivalence, TM-align first generates optimized residue-to-residue alignment based on structural similarity using heuristic dynamic programming iterations. An optimal superposition of the two structures built on the detected alignment, as well as the TM-score value which scales the structural similarity, will be returned.
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-08-16T16:52:21.553Z
Comments.Text: TM-score has the value in (0,1], where 1 indicates a perfect match between two structures. Following strict statistics of structures in the PDB, scores below 0.2 correspond to randomly chosen unrelated proteins while those higher than 0.5 assume generally the same fold in SCOP/CATH.   https://seq2fun.dcmb.med.umich.edu//TM-align/ https://seq2fun.dcmb.med.umich.edu//TM-align/
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-08-16T16:53:18.413Z
Comments.Text: maybe  sequence order independent from the papers.  means tha using with input A,B or B,A returns same result ??
Comments.UserDisplayName: pippo1980
Tags: <phylogenetics><structural-biology>
Title: The difference between sequence-independent and sequence-order independent structural alignment?
ThreadText: # The difference between sequence-independent and sequence-order independent structural alignment?
  
  (Asked by: username_0 on 2022-08-30)
  
  I am confused about the difference between sequence-independent and sequence-order independent structural alignment. TM-align for example claims to be sequence-independent; however, I've seen it is also sequence order independent from the papers. To me, they sound like the same thing, but obviously, they aren't. Does anyone know about anything the difference?
  
  **Tags:** phylogenetics, structural-biology
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: TM-align is an algorithm for sequence independent protein structure comparisons. For two protein structures of unknown equivalence, TM-align first generates optimized residue-to-residue alignment based on structural similarity using heuristic dynamic programming iterations. An optimal superposition of the two structures built on the detected alignment, as well as the TM-score value which scales the structural similarity, will be returned.  
  > **username_2**: TM-score has the value in (0,1], where 1 indicates a perfect match between two structures. Following strict statistics of structures in the PDB, scores below 0.2 correspond to randomly chosen unrelated proteins while those higher than 0.5 assume generally the same fold in SCOP/CATH.   https://seq2fun.dcmb.med.umich.edu//TM-align/ https://seq2fun.dcmb.med.umich.edu//TM-align/  
  > **username_2**: maybe  sequence order independent from the papers.  means tha using with input A,B or B,A returns same result ??  
  
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