Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#6343 closed enhancement (fixed)

Update search of AlphaFold database to January 2022 version

Reported by: Tom Goddard Owned by: Goddard
Priority: moderate Milestone:
Component: Structure Prediction Version:
Keywords: Cc: Zach Pearson
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

EBI made their 3rd update to the AlphaFold database on January 27, 2022, now up to 992316 sequences, about 200,000 more than November 29, 2021 database.

Need to update the BLAST and BLAT alphafold search databases on plato for ChimeraX.

Change History (4)

comment:1 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

Updated and tested. BLAST search of AlphaFold now takes 60 seconds.

comment:2 by Zach Pearson, 4 years ago

Please let me know if you encounter any errors parsing the new database. If you did the same procedure as last time to massage the data into the format we expected from the v1 database there should be no trouble. Need to update blastprotein to ask for version 3... perhaps we can query for the newest version and use it automatically.

comment:3 by Eric Pettersen, 4 years ago

Cc: Zach Pearson added; zip removed

in reply to:  4 ; comment:4 by goddard@…, 4 years ago 

The Alphafold database version is still v2.  So no change is needed in the web service or blat cgi script.  I don’t know why the added 200,000 new entries and still call it v2.
Last edited 4 years ago by Tom Goddard (previous) (diff)
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