Opened 4 years ago

Last modified 3 years ago

#6346 assigned enhancement

Speed up AlphaFold search — at Initial Version

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

Description

Currently the "alphafold match" command currently takes about 20 seconds, using BLAT (not BLAST) on the AlphaFold database of 1 million sequences. It hangs ChimeraX while waiting. EBI plans to eventually extend to 100 million sequences. In July of 2021 the database was introduced with 350K sequences and increased to 1 million in January 2022, so it has increased by 650K in 6 months. Search is probably 3 times slower now.

Investigate other search programs that might be faster, such as HMMER or MMSEQS2.

Ideally we'd want search to run under 10 seconds.

Change History (0)

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