<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>

CC BY-SA 4.0
2019-04-05T14:01:53.707Z
2019-04-05T14:01:53.707Z
Chris_Rands
<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>

<phylogenetics><proteins><sequence-analysis><computation>
How to find the position-specific weight matrix (PSWM) for a list of genes having different sizes?
# 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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