Answers.Body: <p>If your sequences are different lengths, this implies a gapped alignment with insertions/deletions. This is not possible with a regular PSSM, so you have to create a separate PSSM for each group of homologous sequences of the same sequence length.</p>
  
  <p>The alternative is to use a different approach that allows gaps like profile HMMs (as implemented in HMMER3 or HH-Suite3).</p>
  
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Answers.CreationDate: 2019-04-05T14:01:53.707Z
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Body: <p>Wiki has the algorithm for finding position-specific weight matrix (PSWM) for a list of nucleotide sequences having an equal number of nucleotide. How do we find the PSSM for a list of nucleotide sequences having different sizes?</p>
  
Tags: <phylogenetics><proteins><sequence-analysis><computation>
Title: How to find the position-specific weight matrix (PSWM) for a list of genes having different sizes?
ThreadText: # How to find the position-specific weight matrix (PSWM) for a list of genes having different sizes?
  
  (Asked by: username_0 on 2019-04-05)
  
  Wiki has the algorithm for finding position-specific weight matrix (PSWM) for a list of nucleotide sequences having an equal number of nucleotide. How do we find the PSSM for a list of nucleotide sequences having different sizes?
  
  **Tags:** phylogenetics, proteins, sequence-analysis, computation
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2019-04-05. Score: 3
  
  If your sequences are different lengths, this implies a gapped alignment with insertions/deletions. This is not possible with a regular PSSM, so you have to create a separate PSSM for each group of homologous sequences of the same sequence length.
  
  The alternative is to use a different approach that allows gaps like profile HMMs (as implemented in HMMER3 or HH-Suite3).
  
  
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