Changes between Initial Version and Version 1 of Ticket #6346


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Timestamp:
Mar 9, 2022, 4:38:48 PM (4 years ago)
Author:
Tom Goddard
Comment:

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  • Ticket #6346 – Description

    initial v1  
    1 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.
     1Currently the "alphafold match" command currently takes about 12 seconds, using BLAT (not BLAST) on 7PUA chain DX on the AlphaFold database of 1 million sequences.  It hangs ChimeraX while waiting.  It takes about the same time for searching 73 sequences (all of 7PUA).  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.
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    33Investigate other search programs that might be faster, such as HMMER or MMSEQS2.
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    5 Ideally we'd want search to run under 10 seconds.
     5Ideally we'd want search to run under 10 seconds even as more sequences are added.
     6
     7The "alphafold search" command using BLAST currently takes about 6 seconds on 7PUA chain DX.