[Bioperl-l] ncbi blast -V T option

Alexander Kozik akozik at atgc.org
Sat Apr 21 13:40:47 EDT 2007

Hi all,

It was many postings about parsing problems of stand-alone (local) NCBI 
Blast output of version 2.2.15 or later. Recently, I (re?)-discovered 
that Blast option '-V T' fixes the problem with old parsers I have. 
Option '-V T' generates detailed statistics after _each_ query sequence 
in Blast output, like:
... ... ...
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,650,109
Number of Sequences: 26534
Number of extensions: 430364
Number of successful extensions: 1496
Number of sequences better than 1.0e-020: 1
Number of HSP's better than  0.0 without gapping: 1400
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 1495
length of database: 11,047,616
effective HSP length: 96
effective length of database: 8,500,352
effective search space used: 1275052800
frameshift window, decay const: 40,  0.1
... ... ...

Option '-V F' (default) will generate statistics at the end of batch 
Blast output summarizing all query hits together.

Did I miss something from previous postings?
Sorry, if it was already discussed.


Alexander Kozik
Bioinformatics Specialist
Genome and Biomedical Sciences Facility
451 East Health Sciences Drive
University of California
Davis, CA 95616-8816
Phone: (530) 754-9127
email#1: akozik at atgc.org
email#2: akozik at gmail.com
web: http://www.atgc.org/

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