Body: <p>Just like, PSI-BLAST is avaialble to generate a PSSM matrix for peptides, is there a web server where we can generate PSSM for DNA/RNA? I want to find homologous sequences to a given RNA sequence.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-21T08:05:12.103Z
Comments.Text: Please [edit] your question and explain what your final objective is here. How would you use this matrix? To do what? The choice of tool and approach will depend on what you are actually trying to do.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-22T00:46:33.723Z
Comments.Text: Not a web server, but a method is available in biopython to do produce PSSMs. I've used it a number of times and it works well as far as I can tell.
Comments.UserDisplayName: user3479780
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-22T05:55:21.837Z
Comments.Text: thanks, but I believe the biopython method caters to DNA sequences only. But that might help as well.
Comments.UserDisplayName: majumderS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-22T05:56:20.217Z
Comments.Text: @terdon sure I have edited.
Comments.UserDisplayName: majumderS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-09-22T07:29:38.280Z
Comments.Text: Is this RNA translated? If so, it would make more sense to search using tools like tblastn.  Does it have a specific structure? If so, you can use tools that look for similar structures. Do you have multiple homologs of it? Aligned? Or are you starting from a single sequences? What does the RNA do? Depending on what it does, you would focus on different features when looking for homologs.
Comments.UserDisplayName: terdon
Tags: <rna><pssm><dna>
Title: Is there a method/web server to generate Position-specific scoring matrix (PSSM) for nucleotide sequences (DNA/RNA)?
ThreadText: # Is there a method/web server to generate Position-specific scoring matrix (PSSM) for nucleotide sequences (DNA/RNA)?
  
  (Asked by: username_0 on 2023-09-21)
  
  Just like, PSI-BLAST is avaialble to generate a PSSM matrix for peptides, is there a web server where we can generate PSSM for DNA/RNA? I want to find homologous sequences to a given RNA sequence.
  
  **Tags:** rna, pssm, dna
  
  > **Comments:**
  > **username_1**: Please [edit] your question and explain what your final objective is here. How would you use this matrix? To do what? The choice of tool and approach will depend on what you are actually trying to do.  
  > **username_2**: Not a web server, but a method is available in biopython to do produce PSSMs. I've used it a number of times and it works well as far as I can tell.  
  > **username_0**: thanks, but I believe the biopython method caters to DNA sequences only. But that might help as well.  
  > **username_0**: @username_1 sure I have edited.  
  > **username_1**: Is this RNA translated? If so, it would make more sense to search using tools like tblastn.  Does it have a specific structure? If so, you can use tools that look for similar structures. Do you have multiple homologs of it? Aligned? Or are you starting from a single sequences? What does the RNA do? Depending on what it does, you would focus on different features when looking for homologs.  
  
  ---
  
  ## 0 answers
  
  