Monday, December 13, 2021

Omicron (B.1.1.529) protein sequence FASTA and PROSIT spectral libraries!

Want a FASTA for Omicron? Download the NCBI data packet here

Want a PROSIT generated spectral library? You can download one made off of the NCBI data packet here. Overview of settings and how I made it are below. 

Permanent link to zip file on my Google drive in case PROSIT online hosting isn't forever. 

This may not be perfect, but it's something you can find in less than an hour on Google. 

Disclaimers are over there. -->

I feel some guilt for what I initially thought about the person who contacted me asking if I knew where to get the Protein FASTA for the SARS-CoV-2 Omicron (B.1.1.529) variant in the news. It's been two years and there are 4,000 funded programs to make these sequences available. Obviously it is super easy to find these new sequences. Right???  

Then what I thought would take me from 3:30 - 3:35 AM (mostly finding that gif that shows you how to type things into Google) took a whole lot longer. 

Big shoutout, in particular, to this team who made a protein FASTA and in their rush to have the first paper on biorxiv didn't have time to make anything useful downloadable. 

After about an hour of looking at pretty and flashy new sites completely dedicated to SARS-CoV-2 that are mostly news bites about how much they've contributed to the pandemic and thinking for the 7 millionth time that I need to get my swearing back under control before my kid's first word is an f-bomb, I went back to exactly where I got my first SARS-CoV-2 FASTA 2 years ago, the trusty ol' NCBI. The format of the site hasn't changed since I first used it for a class project in the 1990s, the search bar hasn't improved in it's ability to find what you're looking for, but--as always -- what you're looking for is there. 

I made the PROSIT peptide.CSV input with EncyclopeDIA using these settings 

Then I did deep learning magic using the PROSIT online server using these settings. (More thorough instructions for using both of these tools here). 

You can download the PROSIT spectral libraries for Omicron here. 

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