[Bioperl-l] standalone blast composition based statistics parameter

[Fernan Aguero]

+----[ Hubert Prielinger <hubert.prielinger at gmx.at> (03.Feb.2006 21:06):
|
| Hi,
| Does anybody know whether it is possible to perform a with the 
| standalone blast a database search where the composition based 
| statistics parameter is on
| and what's the abbreviation for the parameter
| 
| thanks
| Hubert
|
+----]

only for tblastn.

As Torsten said, 'blastall' with no arguments would have
revealed it: 

[ ... ]
  -C  Use composition-based statistics for tblastn:
      D or d: default (equivalent to F)
      0 or F or f: no composition-based statistics
      1 or T or t: Composition-based statistics as in NAR 29:2994-3005, 2001
      2: Composition-based score adjustment as in Bioinformatics 21:902-911,
          2005, conditioned on sequence properties
      3: Composition-based score adjustment as in Bioinformatics 21:902-911,
          2005, unconditionally
      For programs other than tblastn, must either be absent or be D, F or 0.
      [String]
    default = D

Fernan

PS: this is using the latest BLAST 2.2.13 (ncbi-toolkit 20051206)