[BiO BB] BLAST problems/Questions
Rajkumar.Bondugula at gmail.com
Tue Sep 28 15:43:53 EDT 2004
Thankyou very much for your answers.
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 ...
> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
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