[Bioperl-l] standalone blast composition based statistics parameter

[Hubert Prielinger]

Hi,
thank you very much, If I use the tblastn instead of blastp, I get the 
following error message

[blastall] WARNING: : Unable to open nr.00.nin

I looked up in the folder, but I don't have that file, and if I download 
the database and extract the file, it isn't there either...

thanks

Hubert

Fernan Aguero wrote:

>+----[ 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)
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