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I am thinking of reconstructing an multiple sequence alignment (MSA) of protein sequences from a position-Specific Scoring Matrices (PSSM).

Is it possible? I suppose co-evolution information is lost in PSSM so maybe it is difficult?

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    $\begingroup$ I edited the question to explain what the acronyms represented. $\endgroup$
    – M__
    Mar 19, 2022 at 0:00

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In short I'm afraid it isn't possible because you lose the linkage per Haplotype which is the core information and vital for any population genetics or phylogenetic analysis.

Position-specific scoring matrix e.g. A .60 C .20 G .20 T 0 I tried to produce a position scoring matrix, but it didn't work out, anyway the allele frequency for each e.g. amino acid are given for each alignment position.

You could produce a consensus sequence which, albeit be hypothetical, it might be of some use to understand the generic behaviour of all the sequences in your sample.

Here's a cartoon describing linkage and its importance,

enter image description here

For a multiple sequence alignment of course AB and ab are amino acid residues within the same locus. PSSM could be used to construct a matrix to analyses an established alignment, but that's a fairly complicated Phylogenetics calculation (and a separate question).

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    $\begingroup$ Thank you for the explanation from the perspective of linkage! $\endgroup$
    – Johnny Tam
    Mar 19, 2022 at 13:27
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    $\begingroup$ You are very welcome @JohnnyTam let me know if you have further questions (posted separately of course as per SE rules). $\endgroup$
    – M__
    Mar 19, 2022 at 13:30

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