[BiO BB] Search a Profile against a sequence database

[Raj]

Golhar,
       I need a gapless alignment. PSIBLAST does not have a gapless
alignment option. Thanks for the answer though.

Regards,
Raj


On Wed, 8 Sep 2004 17:27:43 -0400, Ryan Golhar <ryangolhar at hotmail.com> wrote:
> You can use PSI-BLAST.  Generate your sequence database using formatdb
> from the NCBI toolkit, and then use PSI-BLAST to search your custom
> database using your profile...
> 
> -----
> Ryan Golhar
> Computational Biologist
> The Informatics Institute at
> The University of Medicine & Dentistry of NJ
> 
> Phone: 973-972-5034
> Fax: 973-972-7412
> Email: golharam at umdnj.edu
> 
> 
> 

> 
> Hi all,
>      I am looking for some tool that enables me to search a (custom)
> sequence database using the 'profile' (BLAST generated) of the query
> sequence rather than a query sequence itself. If anyone is aware of any
> such tool, please let me know.
> 
> Regards,
> Raj
>