How can I BLAST against my own sequences or a database that isn’t part of NCBI?

You can set up a custom BLAST database using sequences you already have in your Geneious database, or from a FASTA file of sequences you have downloaded from elsewhere.  You first need to set up the custom BLAST service under Tools→Add/Remove Databases→Set up Search Services.  To create the custom database use Tools→Add/Remove Databases→Add Sequence Database.  The Geneious User Manual has more detailed information on how to set this up.  

Note, if you wish to create pre-formatted BLAST databases from fasta files outside of Geneious, you can also run the BLAST+ executables from the command line using the makeblastdb command.  Then put the formatted BLAST database files which are created (there will be multiple files per database) in the BLAST/data folder that was created in your Geneious Data folder when you set up custom BLAST, restart Geneious and the new database will show up when you run custom BLAST.  However, if the database is formatted manually using makeblastdb, there will be no annotations on the resulting alignments. If it is formatted from within Geneious, then an extra file is created with the annotations so Geneious can put them back onto the alignments after a search.

 

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Comments

  • Avatar
    Rodham Tulloss

    The documentation of custom databases is fairly clear.  And being able to BLAST against a set of sequences in a custom database is something that is very useful to me.  There are a few points that the documentation that I can find does not address.  If these features exist, I'd like to find them.  If they don't exist, I'd like to suggest them.  It seems to me that they probably would not be difficult to implement.

    1.  It seems that a database is restricted to contents of a single folder.  Is this true?

    2. Is it possible to create a union of custom databases in order to facilitate crossing of folder boundaries and make a big, cross-folder database?

    3.. Is it possible to make additions of sequences directly to an existing custom database?

  • Avatar
    Helen Shearman

    Thank you for your feedback.  It's great to hear that you are finding the custom BLAST databases useful.

    It is already possible to create a custom BLAST database using sequences from across multiple folders in Geneious.  To select multiple folders at a time in Geneious, hold down Ctrl or Cmd when selecting folders in the sources panel.  The contents of all of the selected folders will appear in the documents table and you can select the sequences you would like to use to create the custom BLAST database.

    It is not currently possible to search across multiple custom BLAST databases at once in Geneious or add sequences to an existing custom BLAST database.  I have passed these suggestions on to the developers.  You can also add your vote and/or comments to this post on our feature request forum for the issue of grouping custom BLAST databases.

  • Avatar
    Christian

    Hi,

    Some it's not working in my case. I use the option Tools→Add/Remove Databases→Set up Search Services and let Geneious make the setup. The program download Blast+ v2.2.29 and then uncompress the .gz files in the selected folder, creating the data, bin, doc subfolders and license and readmefiles. After that, I exit form Geneious and copy my already formated blast databases to the created data/ folder. When I start Geneious again and go to search options, Custom Blast are in grey and with "No database for query".

    What I'm doing wrong?

    Christian.

  • Avatar
    Hilary Miller

    In some instances you need to add ".nt" or ".aa" (for nucleotide or protein respectively) to the file suffixes on your preformatted database files, so that they look as in the screenshot below.  We'll be making some changes to the next major update so that you won't have to do this.  

    Screen_Shot_2014-11-26_at_11.33.12_AM.png 

  • Avatar
    Christian

    Great.. works now!

     

    Thanks Hilary.

  • Avatar
    malcolm cook

    Would it work to reset the NCBI BLAST URL http address to point to a local implementation (made by reverse engineering NCBI QBLAST URL service as documented here: http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html  )

     

  • Avatar
    Hilary Miller

    Yes, it should be possible to point the BLAST URL to a local mirror.  You can also try downloading the preformatted nr/nt databases and use custom BLAST as described here.  However, this can be quite slow. 

  • Avatar
    Luis Peña

    So one question, trying to do the custom BLAST setup all I have is a message "Download halted due to network problems". Geneious is already allowed to access Internet, although the IT services are the ones setting this up for me (I have no admin credentials) Geneious can access NCBI, download genes and genomes and the sort of stuff like that. I also check different folders in case is a writing permit issue. What else could be, different ports being used for set up the database?

    Thanks for your suggestions.

  • Avatar
    Malcolm Cook

    Hi - it would be ideal to be able to keep "Setup Search Services" settings for NCBI intact, and be able to blend in additional blast databases that we serve locally (such as from in-house genome sequencing projects).  Any chance of that?  Thanks!

  • Avatar
    Hilary Miller

    Hi Luis

    When you get the "download halted" error, can you try leaving it for 5-10 min, and see if it restarts downloading again by itself?  We've had a few reports of this, and we're not sure if its an issue from the NCBI server or the Geneious end.  However in some cases the download resumes normally after a few minutes. 

     

  • Avatar
    Hilary Miller

    Hi Malcolm

    What you are describing can be done via Custom BLAST.  You don't need to change anything in the NCBI search settings, but under "Set up Search Services" change the Service to custom BLAST and download and setup the local executables.  Once its installed you can add local databases either via the "Add Database" option in the Geneious menu, or if you already have preformatted BLAST databases that you run outside of Geneious, you can copy them into the BLAST/data folder in your Geneious data folder, as described in the beginning of this thread.   

    However, you can't BLAST to both NCBI and your local databases at the same time as they operate via different routes.

     

     

  • Avatar
    Malcolm Cook

    Hi - my blast server is a different computer than the users desktops on which they are running Geneious.  So, I want Geneious to use the URL/API to my blast server, just like it is using the URL/API to NCBI's blast servers.  That is why I want multiple Search Services.  Make sense now?

  • Avatar
    Hilary Miller

    At the moment we only allow switching between BLAST servers, rather than adding an additional one.  If the API you are using is wwwblast then you can point NCBI BLAST to this instead of NCBI, but not do both at once.  

    I'll forward your request for additional servers to the developers. 

  • Avatar
    Luis Peña

    Hi Hilary thanks for your reply. It didn't worked, its been running the whole day and the progress bar hasn't moved an inch.

  • Avatar
    Hilary Miller

    Hi Luis

    Try getting the executables directly from the NCBI FTP site

    ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

    Make sure you get the correct binary for your operating system.  

    Once you have downloaded the Blast+ binary package, unpack the archive then move the entire Blast+ folder to a location of your choice.  Normally it would go into your Geneious data folder, in your User directory, but you can put it anywhere as long as you point Geneious to the correct location.  Then in your Set up Search Services Window use the Browse button to point Geneious at the Blast folder.