Custom BLAST doesn't find any hits when it should

Occasionally users on Windows may find that custom BLAST reports no hits, even when using a sequence contained in the BLAST database as the query. To fix this, try the following: 

  1. Reinstall the custom BLAST executable to a new location. To do this, go to Tools->Add/Remove Databases->Set up Search Services, and type in a new folder name for the location of custom BLAST (e.g. Users/Username/Geneious 7.1 Data/BLAST2).  Click OK to let Geneious do the setup. Then try making your database again.

  2. If option 1 doesn't fix the issue, you may need to install the 32-bit BLAST executables instead of the default 64-bit executables.  To do this, delete your existing custom BLAST folder(s) from your Geneious Data folder, then manually download the win32 version of BLAST (ncbi-bast-2.2.29+-win32, available from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/).  Extract this file to your data folder. Then go into Set up Search Services and point Geneious to this location (which should be Users/Username/Geneious 7.1 Data/Blast).  You will then need to remake your databases again. 

 

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Comments

  • Avatar
    Pouda Panahandeh

    Hi,

    I tried both options and it did not work again. Is there any other option?

    Thanks,

    Pouda

  • Avatar
    Hilary Miller

    Try the using the version 2.2.28+ executables instead.  You can download these from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.28/.  Then follow the instructions for option 2 above to set up a new folder for custom BLAST.