Changes between Version 1 and Version 2 of Ticket #7358, comment 2


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Timestamp:
Jul 29, 2022, 4:05:32 PM (3 years ago)
Author:
Tom Goddard

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  • Ticket #7358, comment 2

    v1 v2  
    33https://www.ebi.ac.uk/Tools/sss/fasta/
    44
    5 to search for AlphaFold models.  This uses the FASTA algorithm for searching (similar speed to BLAST) and offers about 10 other old choices, but not mmseqs2.  I've started a test run searching alphafold db using their service to see how long it takes.  I'll report the time here when it finishes.
     5to search for AlphaFold models.  This uses the FASTA algorithm for searching (similar speed to BLAST) and offers about 10 other old choices, but not mmseqs2.  I've started a test run searching alphafold db using their service to see how long it takes. Took 10 minutes using 139 residue sequence of 7n7g producing 50 hits and it gave a description for each hit (e.g. "Fosfomycin resistance protein FosB UA=A0A286KC67 UI=A0A286KC67_ENTAV OS=Enterococcus avium OX=33945 GN=fosB").  The FASTA output reported these stats
     6
     7{{{
     8139 residues in 1 query   sequences
     969001092509 residues in 214684311 library sequences
     10 Tcomplib [36.3.8h May, 2020] (32 proc in memory [15G])
     11 start: Fri Jul 29 22:52:04 2022 done: Fri Jul 29 23:01:45 2022
     12 Total Scan time: 2141.080 Total Display time:  0.050
     13
     14Function used was FASTA [36.3.8h May, 2020]
     15}}}
    616
    717Should also try a UniRef90 search.  It probably won't be any faster, but AlphaFold DB mostly covers UniRef90 and possibly EBI has UniRef90 search more heavily optimized.