[BiO BB] BLAST problems/Questions

Raj Rajkumar.Bondugula at gmail.com
Tue Sep 28 15:43:53 EDT 2004


Mackey,

        Thankyou very much for your answers.

Regards,
Raj

On Mon, 27 Sep 2004 15:32:10 -0400, Aaron J. Mackey
<amackey at pcbi.upenn.edu> wrote:
> 
> >    Why am I getting these messages, will these messages effect my
> > results in anyway?
> 
> These are "positive" notifications: everything worked fine.  Checkpoint
> file usage is still considered "experimental" by NCBI, so these
> "debugging" statements are still there.  Ignore them (unless it says
> "unsuccessful", of course).
> 
> > Why is this happening? is there anyway to have just ungapped alignment
> > while searching?
> 
> BLAST is a gap-capable algorithm; the fact that you've given it a
> profile instead of a "flat" scoring matrix doesn't change anything.  If
> you'd like to prevent gaps, try raising the gap penalties ...
> 
> -Aaron
> 
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