Run BLAST search

BeeDeeM automatically converts all sequence databanks to a BLAST databank.

BLAST bank format

BeeDeeM uses NCBI's makeblastdb tool to prepare BLAST databanks, so they can be directly used with the BLAST suite of softwares; either legacy BLAST (blastall program) or BLAST+.

Command-line use of BLAST

We suppose BLAST is already installed on your system.

Let us suppose you have installed the PDB databank using BeeDeeM. Following the Databanks organization, it is installed in directory:

${biobaseRootDir}/p/PDB_proteins/current/PDB_proteins

Say, you have a query file containing some protein sequences: p12265.fas

Now, to run a BLAST search, simply use this command:

blastp \
      -db ${biobaseRootDir}/p/PDB_proteins/current/PDB_proteins/PDB_proteinsM \
      -query p12265.fas \
      -outfmt 5 \
      -out result.xml

Of course, adapt the command-line to your needs.

The important point here, is the name of the BLAST bank. In the directory where PDB is installed, we locate the file ending with M.pal: this is the BLAST bank alias file name to provide to BLAST.

In you have a nucleotide bank installed, look for file ending with M.nal instead.

Sample use case.

View BLAST results

BLAST results prepared using '-outfmt 5' argument (see command-line, above) are XML files that can be viewed with BLAST Viewer.

Quickly locate BLAST banks

You can use info tool to get the list of BLAST banks. Read more.