Setting up shared BLAST for multiple users

There are several ways to set up shared BLAST databases for your organisation depending on what you have available. They are:


1. Geneious "Custom BLAST" on a network drive

As described in the post How can I BLAST to a local copy of the NCBI nr or nt databases, a local copy of the BLAST executables can easily be set up to search a local copy of any databases you need. This approach can be used to create shared databases by simply putting the BLAST executables and associated data on a network drive.

Each user can then follow the same instructions for setting up Custom BLAST to access the databases. Their CPU will do the work but that data will be centralised. It is possible that this could cause performance issues over the network though and you'll need to deal with ownership and ensure that your users don't try adding databases themselves.

It is also possible to create BLAST databases outside of Geneious, by running the BLAST+ executable from the command line and using the makeblastdb command.  Then put the formatted BLAST database files into the BLAST/data folder where your other custom BLAST databases are located and Geneious users will be able to see them when they run custom BLAST.  Note that 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.

2. Raw database files on a network drive

Another approach is to provide users with a set of sequences in FASTA format that they can create a Custom BLAST database from and keep that up to date and have them replace their local copies. This has the advantage that it is essentially purely parallel so it will scale indefinitely but it has the disadvantage that you can't be sure they're all searching the same database.

3. Local mirror of NCBI webservices

If you have a mirror of NCBI's BLAST web service running on your local network (such as WWWBLAST) then Geneious can be set to use this instead of NCBI's public servers:

  1. Go to Tools → Add/Remove Databases → Set Up BLAST Services
  2. Choose NCBI using the service drop-down box at the top of the dialog
  3. Enter the URL for your BLAST server
  4. If your mirror has different databases to NCBI, click the Edit Databases button to set them up
  5. Click OK to save

Now, whenever a search is performed by clicking BLAST in the toolbar and choosing an NCBI database, the query will be sent to your local server instead.

4. Geneious Server BLAST

Geneious Server is a software package that extends the capability of Geneious to take advantage of your existing enterprise level infrastructure. It comes at an additional cost and includes the ability to create and manage shared BLAST databases.






Have more questions? Submit a request