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?
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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).
