Blast databases are hosted on nextgen.shore.mbari.org. The username is geneadm, for the password see Sebastian Sudek, Mike McCann, Brian Schlining, or Rich Schramm.

To create new blast databases:

1. Get the protein or nucleotide sequences in FASTA format
2. Remove or replace all pipe symbols (|) from the sequence ID (which is anything before the first space in the fasta header)
3. Create sequence IDs that do not occur in any of the other databases. For example, you should not have two separate blast databases with IDs like >CCMP2099_1. Sequence IDs can be rather long, so for instance add the sample ID to them: >MMETSP0022C_CCMP2099_1
4. Copy the sequences to the /data/meta (for metatranscriptome and metagenome files) or /data/dbs (for everything else) on nextgen.shore.mbari.org. This can be done using ssh from another computer with username geneadm and password

   scp path/to/fasta geneadm@nextgen.shore.mbari.org:/data/meta
   

5. Login to nextgen and go to the directory with the sequences

   ssh geneadm@nextgen.shore.mbari.org (same password)
   cd /data/dbs (or meta)
   

6. Run

   makeblastdb -dbtype nucl -in <new nucleotide fasta> -title <blast db name you want> -parse_seqids
   

   For protein sequences, dbtype is prot

7. Restart the sequence server with

   sudo /sbin/service httpd restart
   

   This will ask you for the password again

8. Log out with

   exit
   

To remove databases, simply remove the files created by makeblastdb and restart the server.