Some notes on how to run blast+

  • We use psiblast 2.3+

    The old (‘legacy version’) blast (blastpgp command) is no longer supported; BioShell package is being adapted to the newest version of psiblast toolkit.

  • Running psiblast directly

    Example script that runs the new psiblast command is given below:

    /home/bioshell_server/TOOLS/blast+/bin/psiblast -num_iterations 5 \
          -num_alignments 100000 \
          -num_descriptions 100000 \
          -max_hsps 0 \
          -inclusion_ethresh 0.000001 \
          -evalue 0.000001 \
          -db /home/bioshell_server/TOOLS/blast+/data/nr \
          -query ./$DIR/$TARGET.fasta \
          -show_gis  -outfmt 0 \
          -num_threads 12 \
          -out ./$DIR/$TARGET.psi \
          -out_pssm ./$DIR/$TARGET.asn1 \
          -out_ascii_pssm ./$DIR/$TARGET.fasta.mat

On the contrary to the original blastpgp command, now the names of command line parameters are quite self-explanatory. One of the advantages of the new version of blast is its parallel implementation allowing run a single job below a minute. Resulting sequence profiles are now stored in ASN.1 format, which is supported by BioShell.