Get cleaved SARS-CoV-2 protein sequences (all major variants)?
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3 days ago
ngarber • 0

I have an algorithm for assessing the presence of a degenerate motif in lists of protein sequences, and I would like to run it on SARS-CoV-2 proteins.

However, some SARS-CoV-2 proteins are cleaved post-translation to make multiple functional proteins. Is there a way to get the post-cleavage list of protein sequences?

Ideally I'd like this to be for all proteins from all major variants, but not have a gargantuan amount of data. There are almost a million sequenced SARS-CoV-2 genomes now, and that's more than my poor old laptop can handle! So if there was a way to, say, get reference consensus sequences (like RefSeq, except RefSeq doesn't have variants) for the major variants (alpha, delta, omicron, omicron subvariants BA.4 and BA.5, etc.), that would be really helpful.

I'm working in Python, so I can either download through Python or use a website, either is fine. Thanks!

motif variant Python SARS-CoV-2 cleavage • 164 views
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Not sure if this is what you are looking for but you can get protein sequences from EBI Covid Portal: https://www.covid19dataportal.org/proteins?crossReferencesOption=all

There is also NCBI's SARS protein portal section: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Protein&VirusLineage_ss=Severe%20acute%20respiratory%20syndrome%20coronavirus%202,%20taxid:2697049

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