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Database of precomputed MSAs? #292

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GXcells opened this issue Feb 7, 2025 · 1 comment

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GXcells commented Feb 7, 2025

I was wondering if there are available database of precomputed MSAs for example for all human proteins?

It seems to me that it is a waste of time , ressources anf energy thay everyone have to compute MSAs each time for a prediction.

Or could you let me know what could be the rational for not having/not using such precomputed MSAs ?

Augustin-Zidek added the question label

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Augustin-Zidek commented Feb 7, 2025

I was wondering if there are available database of precomputed MSAs for example for all human proteins?

There is not, as far as I am aware.

Or could you let me know what could be the rational for not having/not using such precomputed MSAs?

There is AlphaFold Database that provides AlphaFold 2 structure prediction for almost all UniProt proteins.
Many servers that compute MSA have local caching, hence they don't recompute MSA for the same sequence.
Protein sequence databases grow and change (e.g. UniProt/UniRef/MGnify has 4-5x releases per year), hence if you wanted to always run against the latest db, that would require recomputing the MSAs multiple times a year anyway.

Augustin-Zidek closed this as completed

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