Parsing a local blast result

Question

[imaditi1987]

When we perform a ncbi blast on its server the output is something like below: The local blast setup that we use (BLAST-2.3.0+) gives us the speed but I believe that we can only parse the hsps which may be many for a single subject. How can we get the max score,total score, e-value,identity, accession as shown above in a tabular form?.

[GenoMax]

Look into usin option -outfmt 6 (and its extensions). More information is in blast handbook (Table c-1).

Blast is currently in v.2.6.0. You should upgrade if you can.

[imaditi1987]

Thanks for the reply. I have been using outfmt 6 option but the output it gives is in terms of hsp (hsp evalue, hsp length, hsp bit score etc). I would want the combined total bit score.

[Jake Warner]

I'm not sure what a combined bit score would be but from the above it sounds like you might want just the top hit? You can look into the max_hsps and max_target_seqs options.

[BioinfGuru]

Ah good old perl homework... I wish every bioinf pipe was as easy as this.

"Read a FASTA protein sequence from file (test file given) and use this sequence for a standalone BLAST search against swissprot at NCBI. Parse the BLAST output and for the top ten hits print the sequence identifier, score, E-value and % sequence identity (that is between Query and Hit)."

Bioperl is your buddy:

use Bio::Tools::Run::RemoteBlast;   # For running the blast search
use Bio::SearchIO;  # for parsing the blast report