[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.

-Alex

-- 
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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