[Bioperl-l] ncbi blast -V T option
akozik at atgc.org
Sat Apr 21 13:40:47 EDT 2007
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:
... ... ...
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.
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email#1: akozik at atgc.org
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